The second stage of phase refinement is based on 'phase annealing' (Sheldrick, 1990. This has proved to be an efficient search method for large structures, and possesses a number of beneficial side-effects. It is based on steps cycles of tangent formula refinement (one cycle is a pass through all ns phases), in which a correction is applied to the tangent formula phase. The phase annealing algorithm gives the magnitude of the correction (it is larger when the 'temperature' is higher; this corresponds to a larger value of Boltz), and the sign is chosen to give the best agreement with the negative quartets (if there are no negative quartets involving the reflection in question, a random sign is used instead). After each cycle through all ns phases, a new value for Boltz is obtained by multiplying the old value by cool; this corresponds to a reduction in the 'temperature'. To save time, only ns reflections are refined using the strongest t^mtpr^t triplets and t^mnqr^t quartets for each reflection (or less, if not so many phase relations can be found). The phase annealing parameters chosen by the program will rarely need to be altered; however if poor convergence is observed, the t^Boltz^t value should be reduced; it should usually be in the range 0.2 to 0.5. When the 'TEXP 0 / TREF' method of multisolution partial structure refinement is employed, Boltz should be set at a somewhat higher value (0.4 to 0.7) so that not too many solutions are duplicated.&&ShelX-97 Manual . . . . . . . . init-help && ~INIT nn [#] nf [#] s+ [0.8] s- [0.2] wr [0.2]~
The first stage involves five cycles of weighted tangent formula refinement (based on triplet phase relations only) starting from nn reflections with random phases and weights of 1. Single phase seminvariants which have S1-formula P+ values less that s- or greater than s+ are included with their predicted phases and unit weights. All these reflections are held fixed during the INIT stage but refined freely in the subsequent stages. The remaining reflections also start from random phases with initial weights wr, but both the phases and the weights are allowed to vary.
If nf is non-zero, the nf 'best' (based on the negative quartet and triplet consistency) phase sets are retained and the process repeated for (npp-nf) parallel phase sets, where npp is the previous number of phase sets processed in parallel (often 128). This is repeated for nf fewer phase sets each time until only a quarter of the original number are processed in parallel. This rather involved algorithm is required to make efficient use of available computer memory. Typically nf should be 8 or 16 for 128 parallel permutations.
The purpose of the INIT stage is to feed the phase annealing stage with relatively self-consistent phase sets, which turns out to be more efficient than starting the phase annealing from purely random phases. If TREF 0 is used to generate partial structure phases for all reflections, the INIT stage is skipped. To save time, only ns reflections and the strongest mtpr triplets for each reflection (or less, if not so many can be found) are used in the INIT stage; these numbers are given on the PHAN instruction. && ShelX-97 Manual . . . . . . . . TREF-help **np,nE,kapscal,ntan,wn**&& ~TREF np [100] nE [#] kapscal [#] ntan [#] wn [#]~
np is the number of direct methods attempts; if negative, only the solution with code number |np| is generated (the code number is in fact a random number seed). Since the random number generation is very machine dependent, this can only be relied upon to generate the same results when run on the same model of computer. This facility is used to generate E-maps for solutions which do not have the 'best' combined figure of merit. No other parameter may be changed if it is desired to repeat a solution in this way. For difficult structures, it may well be necessary to increase np (e.g. TREF 5000) and of course the computer time allocated for the job.
nE reflections are employed in the full tangent formula phase refinement. Values of nE that give fewer than 20 unique phase relations per reflection for the full phase refinement are not recommended.
kapscal multiplies the products of the three E-values used in triplet phase relations; it may be regarded as a fudge factor to allow for experimental errors and also to discourage overconsistent (uranium atom) solutions in symorphic space groups. If it is negative the cross-term criteria for the negative quartets are relaxed (but all three cross-term reflections must still be measured), and more negative quartets are used in the phase refinement, which is also useful for symorphic space groups.
ntan is the number of cycles of full tangent formula refinement, which follows the phase annealing stage and involves all nE reflections; it may be increased (at the cost of CPU time) if there is evidence that the refinement is not converging well. The tangent formula is modified to avoid overconsistency by applying a correction to the resulting phase of cos-1(<α>/α) when <α> is less than α ; the sign of the correction is chosen to give the best agreement with the negative quartets (a random sign is used if there are no negative quartets involving the phase in question). This tends to drive the figures of merit Rα and Nqual simultaneously to desirable values. If ntan is negative, a penalty function of (<Σ1> - Σ1)2 is added to CFOM (see below) if and only if Σ1 is less than its estimated value <Σ1>. Σ1 is a weighted sum of the products of the expected and observed signs of one-phase seminvariants, normalized so that it must lie in the range -1 to +1. This is useful (i.e. better than nothing) if no negative quartets have been found or if they are unreliable, e.g. when macromolecular ΔF data are employed (see below).
wn is a parameter used in calculating the combined figure of merit CFOM: CFOM = Rα (NQUAL < wn) or Rα+ (wn-NQUAL)2 (NQUAL ≥ wn); wn should be about 0.1 more negative than the anticipated value of NQUAL. If it is known that the measurements of the weak reflections are unreliable (i.e. have high standard deviations), e.g. because data were collected using the default options on a CAD-4 diffractometer, then the NQUAL figure of merit is less reliable. If the space group does not possess translation symmetry, it is essential to obtain good negative quartets, i.e. to measure ALL reflections for an adequate length of time.
Only the TREF instruction is essential to specify direct methods; appropriate INIT, PHAN, FMAP, GRID and PLAN instructions are then generated automatically if not given.&&ShelX-97 Manual . . . . . . . . patt-help && ~PATT nv [#] dmin [#] resl [#] Nsup [#] Zmin [#] maxat [#]~
nv is the number of superposition vectors to be tried; if it is negative the search for possible origin shifts is made more exhaustive by relaxing various tolerances etc. dmin is the minimum allowed length for a heavy-atom to heavy-atom vector; it affects ONLY the choice of superposition vector. If it is negative, the program does not generate any atoms on special positions in stage 4 (useful for some macromolecular problems). resl is the effective resolution in Å as deduced from the reflection data, and is used for setting various tolerances. If the data extend further than the crystal actually diffracted, or if the outer data are incomplete, it may well be worth increasing this number. This parameter can be relatively critical for macromolecular structures. Nsup is the number of unique peaks to be found by searching the superposition function. Zmin is the minimum atomic number to be included as an atom in the crossword table etc. (if this is set too low, the calculation can take appreciably longer). maxat is the maximum number of potential atoms to be included in the crossword table, and can also appreciably affect the time required for PATT. && ShelX-97 Manual . . . . . . . . vect-help && ~VECT X Y Z~
A superposition vector (with coordinates taken from the Patterson peak-list) may be input by hand by a VECT instruction, in which case the first two numbers on the PATT instruction are ignored (except for their signs !), and a PATT instruction will be automatically generated if not present in the .ins file. There may be any number of VECT instructions.
In the unlikely event of a routine PATT run failing to give an acceptable solution, the best approach - after checking the data reduction diagnostics carefully as explained above - is to select several potential heavy-atom to heavy-atom vectors by hand from the Patterson peak-list and specify them on VECT instructions (either in the same job or different jobs according to local circumstances) for use as superposition vectors. The exhaustiveness of the search can also be increased - at a significant cost in computer time - by making the first PATT parameter negative and/or by increasing the value of resl a little. The sign of the second PATT parameter (a negative sign excludes atoms on special positions) and the list of elements which might be present (SFAC/UNIT) should perhaps also be reconsidered. && ShelX-97 Manual . . . . . . . . plan-help && ~PLAN npeaks[20] d1[#] d2[#]~
If npeaks is positive a Fourier peak list is printed and written to the .res file; if it is negative molecule assembly and line printer plots are also performed. Distances involving peaks which are less than r1+r2+d1 (the covalent radii r are defined via SFAC; 1 and 2 refer to the two atoms concerned) are printed and used to define 'molecules' for the line printer plots. Distances involving atoms and/or peaks which are less than r1+r2+|d2| are considered to be 'non-bonded interactions'; however distances in which both atoms are hydrogen or at least one is carbon (recognised by SFAC label 'C') are ignored. These non-bonded interactions are ignored when defining molecules, but the corresponding atoms and distances are included in the line printer output. Thus an atom or peak may appear in more than one map, or more than once on the same map. A table of the appropriate coordinates and symmetry transformations appears at the end of each molecule.
Negative d2 includes hydrogen atoms in the line printer plots, otherwise they are left out (but included in the distance tables). For the purposes of the PLAN instruction, a hydrogen atom is one with a radius of less than 0.4 Å. Peaks are assigned the radius of SFAC type 1, which is usually set to carbon. Peaks appear on the printout as numbers, but in the .res file they are given names beginning with 'Q' and followed by the same numbers. Peak heights are also written to the .res file (after the sof and dummy U values) in electrons Å-3. See also MOLE for forcing molecules (and their environments) to be printed separately. && ShelX-97 Manual . . . . . . . . fmap-help && ~FMAP code[2] axis[#] nl[53]~
The unique unit of the cell for performing the Fourier calculation is set up automatically unless specified by the user using FMAP and GRID; the value of axis must be non-zero to suppress the automatic selection. The program chooses a 53 x 53 x nl or 103 x 103 x nl grid depending on the resolution of the data. axis is1, 2 or 3 to define the direction perpendicular to the layers. Dispersion corrections are applied (so that the resulting electron density is real) and Friedel opposites are merged after the least-squares refinement and analysis of variance but before calculating the Fourier synthesis. This will improve the map (and bring the maximum and minimum residual density closer to zero) compared with SHELX-76. In addition, since usually all the data are employed, reflections with σ (F) relatively large compared with Fc are weighted down. This should be better than the use of an arbitrary cutoff on Fo/σ(F). The rms fluctuation of the map relative to the mean density is also calculated; in the case of a difference map this gives an estimate of the 'noise level' and so may be used to decide whether individual peaks are significant. Usually FMAP 2 is employed to find missing atoms, but if a significant part of the structure is missing, FMAP 5 or 6 may be better. ACTA requires FMAP 2 so that the difference density is on an absolute scale.
If code is made negative, both positive and negative peaks are included in the list, sorted on the absolute value of the peak height. This is intended to be useful for neutron diffraction data.
code = 3: Electron density synthesis with coefficients Fo and phases φ(calc).
code = 4: Electron density synthesis with coefficients (2Fo-Fc) and phases φ(calc). F(000) is included in the Fourier summations for code = 3 and 4.
code = 6: Sim-weighted (2mFo-Fc) Fourier with coefficients sharpened by multplying with
(E/F)1/2.
&&
ShelX-97 Manual . . . . . . . .
acta-help && ~ACTA 2thetafull[#]~
A 'Crystallographic Information File' file name.cif is created in self-defining STAR format. This ASCII file is suitable for data archiving, network transmission, and (with suitable additions) for direct submission for publication. ACTA automatically sets the BOND, FMAP 2, PLAN and LIST 4 instructions, and may not be used with other FMAP or LIST instructions or with a positive OMIT s threshold. A warning message appears if the cell contents on the UNIT instruction are not consistent with the atom list, because they are used to calculate the density etc. which appears in the .cif output file.
2thetafull is used to specify the value of 2Θfor which the program calculates the completeness of the data for the CIF output file as required by Acta Crystallographica. If no value is given, the program uses the maximum value of 2Θ for the reflection data. If the data were collected to a specific limiting 2Θ,or if a limit was imposed using SHEL, this would be a good choice. Otherwise the choice of 2thetafull is a difficult compromise; if it is too low, the paper will be rejected because the resolution of the data is not good enough; if it is higher, the lower completeness might lead to rejection by the automatic Acta rejection software! SHELXL calculates the completeness by counting reflections after merging Friedel opposites and eliminating systematic absences (and the reflection 0,0,0). && ShelX-97 Manual . . . . . . . . cgls-help && ~CGLS nls[0] nrf[0] nextra[0] maxvec[511]~
As L.S., but the Konnert-Hendrickson conjugate-gradient algorithm is employed instead of the full-matrix approach. Although BLOC may be used with CGLS, in practice it is much better to refine all parameters at once. CGLS is much faster than L.S. for a large number of parameters, and so will be the method of choice for most macromolecular refinements. The convergence properties of CGLS are good in the early stages (especially if there are many restraints), but cannot compete with L.S. in the final stages for structures which are small enough for full-matrix refinement. The major disadvantage of CGLS is that it does not provide estimated standard deviations, so that when a large structure has been refined to convergence using CGLS it may beworth performing a blocked full-matrix refinement (L.S./BLOC) to obtain the standard deviations in quantities of interest (e.g. torsion angles, in which case only xyz blocks would be required).The other parameters have the same meaning as with L.S.; CGLS is entirely suitable for Rfree tests (negative nrf), and since it requires much less memory than L.S. there will rarely be any reason to change maxvec from its default value.
The CGLS algorithm is based closely on the procedure described by Hendrickson & Konnert (1980). The structure-factor derivatives contribute only to the diagonal elements of the least-squares matrix, but all 'additional observational equations' (restraints) contribute in full to diagonal and off-diagonal terms, although neither the l.s. matrix A nor the Jacobean J are ever generated. The preconditioning recommended by Hendrickson & Konnert is used to speed up the convergence of the internal conjugate gradient iterations, and has the additional advantage of preventing the excessive damping of poorly determined parameters characteristic of other conjugate gradient algorithms (Tronrud,1992).
A further refinement in the CGLS approach is to save the parameter shifts from the previous CGLS cycle, and to use them to improve the estimated parameter shifts in the current cycle. Since this is only possible in the second and subsequent cycles, an initial shift multiplier of 0.7 is assumed in the first cycle. If the refinement proves to be unstable, this starting value can be reset using the first DAMP parameter.
In addition to this optimization of the CGLS shift multiplication factor, the individual parameter shifts are monitored each L.S. or CGLS cycle, and the shift multiplication factors are reduced (to a value between 0.5 and 1) for parameters that tend to oscillate. This applies only to refinements in which BLOC is not used. This produces an additional improvement in the convergence of the least-squares refinement, but (unlike Marquardt damping) has no effect on esds. && ShelX-97 Manual . . . . . . . . l.s.-help && ~L.S. nls[0] nrf[0] nextra[0] maxvec[511]~
nls cycles of full-matrix least-squares refinement are performed, followed by a structure factor calculation. When L.S. (or CGLS) is combined with BLOC, each cycle involves refinement of a block of parameters which may be set up differently in different cycles. If no L.S. or CGLS instruction is given, 'L.S. 0' is assumed.
If nrf is positive, it is the number of these cycles that should be performed before applying ANIS. This two-stage refinement is particularly suitable for the early stages of least-squares refinement; experience indicates that it is not advisable to let everything go at once!
Negative nrf indicates which reflections should be ignored during the refinement but used instead for the calculation of free R-factors in the final structure factor summation; for example L.S. 4 -10 would ignore every 10th reflection for refinement purposes. It is desirable to use the same negative value of nrf throughout, so that the values of 'R1(free)' and 'wR2(free)' are not biased by the 'memory' of the contribution of these reflections to earlier refinements. These independent R-factors (Brünger, 1992) may be used to calibrate the sigmas for the various classes of restraint, and provide a check as to whether the data are being 'over-refined' (primarily a problem for macromolecules with a poor data to parameter ratio). In SHELXL, these ignored reflections are not used for Fourier calculations.
nrf=-1 selects the Rfree reference set that is flagged (with negative batch numbers) in the .hkl file (SHELXPRO may be used to do this). The division of the data into reference and working set is then independent of the space group and the MERG, OMIT and SHEL settings. However on merging reflections, to play safe a reflection is retained in the reference set only if all equivalents have the Rfree flag set. Thus if equivalents are present, it is a good idea to use the SHELXPRO option to set the Rfree flag in thin shells, so that all equivalents of a particular unique reflection are either all in the reference set or all in the working set. nrf=-1 is the recommended way of applying the Rfree test in SHELXL.
nextra is the number of additional parameters which were derived from the data when performing empirical absorption corrections etc. It should be set to 44 for DIFABS [or 34 without the theta correction; Walker & D. Stuart (1983)]. It ensures that the standard deviations and GooF are estimated correctly; they would be underestimated if the number of extra parameters is not specified. nextra is zero (and so can be omitted) if extra information in the form of indexed crystal faces or psi-scan data was used to apply an absorption correction.
maxvec refers to the maximum number of reflections processed simultaneously in the rate-determining calculations. Usually the program msgizes all available memory to process as many reflections as possible simultaneously, subject to a maximum of maxvec, which may not be larger than 511. For complicated reasons involving the handling of suppressed and 'Rfree' reflections and input/output buffering, some blocks may be smaller than the maximum, especially if the facilities for refinement against twinned or powder data are being used. It may be desirable to set maxvec to a smaller number than 511 to prevent unnecessary disk transfers when large structures are refined on virtual memory systems with limited physical memory. && ShelX-97 Manual . . . . . . . . plop-help && ~PLOP followed by up to 10 numbers~
PLOP specifies the number of peaks to start with in each cycle of the peaklist optimization algorithm of Sheldrick & Gould (1995). Peaks are then eliminated one at a time until either the correlation coefficient cannot be increased any more or 50% of the peaks have been eliminated.
Note: Olex2 calculates sensible default values based on the cell volume && . . . . . . . . mind-help && ~MIND mdis [1.0], mdeq [2.2]~
|mdis| is the shortest distance allowed between atoms for PATS and FIND. If mdis is negative PATFOM is calculated, and the crossword table for the best PATFOM value so far is output to the .lst file. In this case the solution is passed on to the PLOP stage if either the CC is the best so far or the PATFOM is the best so far. mdeq is the minimum distance between symmetry equivalents for FIND (for PATS the |mdis| distance is used). Thus the default setting of mdeq prevents FIND from placing atoms on special positions. This is usually desirable because it helps to avoid pseudo-solutions such as the 'uraninum atom solution' that are incorrect but fit the tangent formula, but it might be better to change this setting to -0.1 to allow special positions; especially for the location of heavy atom sites obtained by (halide) soaking. For PLOP the PREJ instruction can be used to control whether peaks on special positions are selected. && . . . . . . . . ntry-help && ~NTRY ntry [0]~
Number of global tries if starting from random atoms, PATS or GROP. If ntry is zero or absent, the program runs until it is interrupted by writing a name.fin file in the current working directory. && . . . . . . . . find-help && ~FIND na [0], ncy [#]~
Search for na atoms in ncy dual space cycles. If WEED is employed, na is the number of atoms remaining after the random omit. ncy defaults to the largest of (20 or na) or, if PATS is used, to the smaller of (3na and 20). If FIND is absent, PLOP expands directly from the starting atoms.
Note: Olex2 calculates a sensible default value for na based on the cell volume && . . . . . . . . dual-space-info &&Dual Space is a structure solution method&& Sheldrick, G.M. (2008). Acta Cryst. A64, 112-122 . . . . . . . . flip-help && ~interval[60]~
An integer determining how often the algorithm yields the intermediate results. Using the default value of 60, the algorithm yields the intermediate results after every 60th iteration. && . . . . . . && ~interval[60]~
这个整数决定了算法生成中间结果的频率。如默认值60说明了算法每重复60次就生成中介结果。 .
setup-title-0 Welcome to the Olex2 Customisation . . . . . . 欢迎定定义Olex2 .
setup-txt-0 The look and feel of Olex2 can be customised in many different ways.&&@Setup@Stepping through these setup steps will set up many of the features you might wish to modify. 按照这个设置方案一步步进行下去，您将按照您的喜好修改很多要素。 这个设置方案可以在任何时候运行，且所有设置都能在程序的其它地方设定。 .
news-1 The electron density map viewer tool has been updated. The levels shown initially are more sensible, and will show positive and negative regions of the map at the same time. . . . . . . 电子密度图查看器已经更新。这些等级看上去更加合理，并能同时在图中显示正电荷和负电荷区域。 .
news-1-title Interactive Electron Density Viewer . . . . . . 互交式电子密度查看器 .
news-2 Olex2 now propagates errors for calculations involving any distances and angles. . . . . Fehler in der Bestimmung von Abständen, Winkeln und anderen geometrischen Berechnungen werden nun von Olex2 berücksichtigt. . Olex2现在能计算各个键长和键角的误差。 .
news-2-title Errors for Distances and Angles . . . . Abweichungen für Abstände und Winkelberechnungen . 键长键角的误差 .
news-3 When errors occur in Olex2, we would like to know about them. Please use our portal to report any issues you might encounter. . . . . Falls Fehler in Olex2 auftreten, würden wir gerne davon wissen. Bitte lassen informieren sie uns über das Portal. . 欢迎您将在使用Olex2 中发现的任何问题告诉我们。 请通过我们的网站反馈您所碰到的问题。 .
news-3-title Program Errors . . . . Programmfehler . 程序错误 .
news-4 Olex2 will not work with ShelX executables from WinGX. There is not much we can do about this. Please make sure to place non-WinGX versions of ShelX in the installation directory of Olex2. . . . . Olex2 funktioniert nicht mit den ShelX executables von WinGX. Wir können daran leider nichts ändern. Bitte stellen sie sicher, dass sie nicht-WinGX Versionen von ShelX irgendwo auf dem Pfad haben. . Olex2不能运行WinGX 版本的ShelX 可执行文件。 我们暂时也无法解决这个问题，请将非WinGX 版本的ShelX 拷贝至Olex2的安装目录。 .
news-4-title WinGX ShelX Executables . . . . WinGX ShelX Executables . WinGX版本的ShelX可执行文件 .
setup-title-1 Elements of the GUI . . . . . . GUI的各个要素 .
setup-txt-1 &&
@Background@
The background of the main Olex2 window (The OpenGL window) has three states:
~White~ (Toggle with F2)
~Solid Colour~ (Toggle with F2)
~Gradient~ (Switch on/off with F4) Change
@Swap GUI Panel@
The main GUI panel is displayed on the right of the Olex2 window. This panel can be moved to the left:
~Swap Panel~now
@Tooltips@
When placing the mouse over any link in the main GUI panel, a 'Tooltip' will appear if this functionality is switched on. Tooltips can be a good idea when learning how to run Olex2, but might be a bit of a distraction later on.
~Switch Tooltips~ ON/OFF
@Help on Typing@
When typing in the command line, a window listing all the commands starting with the typed letters will appear if this functionality is switched on.
~Switch Help~ ON/OFF
&& . . . . . . . .
setup-title-2 Fonts . . . . . . 字体 .
setup-txt-2 The fonts used in the OpenGL window Olex2 (the main window, where the molecule is displayed) are OpenGL objects. You can choose to use a builtin Olex2 font, or you can opt for any font that is available on your system.
To set the colour of the font, you need to adjust the OpenGL properties of the 'material', out of which the characters of the font are made. Typically, changing the first and second coloured box in the dialoge will be sufficient.
&&
@Console@
Console text consists of various parts
~Console~ Text entered by the user
Olex Font | System Font | Colour
~Errors~ Error messages returned by Olex2
Colour
~External Program~ Output created by external programs
Colour
~Exceptions~ Olex2 Exceptions
Colour
~helpcmd~
Colour
~helptxt~
Olex Font | System Font | Colour
@Labels@
Labels on atoms. These can be simply the atom name, but many different properties of the atoms can be displayed
~Labels~
Font | System Font | Colour
&& . . . . . . . .
setup-title-4 Skins . . . . . . 皮肤 .
setup-txt-4 The overall look and feel of Olex2 can be set by making use of themes, also called skins.
$spy.AvailableSkins() $spy.AvailableSkins()This setup can be run at any time, and all these settings can also be set elsewhere in the program.&& . . . . . .
Olex2可以通过不同的方法自定义外观等。
You can also customise the look of your current installation using the Configuration Tool. Please note that your customisation will be lost when you reload the skin that you have customised. . . . . . . 皮肤，即整个Olex2的外观风格设置所用的主题。
您也可以修改当前您已安装的皮肤－设置工具. 请注意，在您重新载入皮肤后，已做的修改将被丢失。 .
setup-title-3 Plugins . . . . . . 插件 .
setup-txt-3 The functionality of Olex2 can be extended by Olex2 Plugins. Available Plugins are listed below and already installed plugins are highlighted.$spy.AvailablePlugins() . . . . . . Olex2插件将扩展Olex2的已有功能。提供的插件如下所示。已经安装好的将被高亮显示。$spy.AvailablePlugins() .
setup-title-5 External Programs . . . . . . 外部程序 .
setup-txt-5 You may wish to use external programs from within Olex2.
Olex2 will find any relevant program either because it is on the system
path of your computer or because you have put it into the base directory
of your Olex2 Program Directory.
The following programs are currently 'known' to exist:
&&
~SADABS (Bruker Only)~
$file.which(SADABS.exe)
~XP (Bruker Only)~
$file.which(shelxp.exe)
$file.which(xp.exe)
~ShelXS~
$file.which(shelxs.exe)
~XS (Bruker Version)~
$file.which(xs.exe)
~ShelXD~
$file.which(shelxd.exe)
~XM (Bruker Version)~
$file.which(xm.exe)
~ShelXL~
$file.which(shelxl.exe)
~XL (Bruker Version)~
$file.which(xl.exe)
&& . . . . . . 您也许需要在Olex2中使用外部程序。Olex2将找到任何相关联的程序，如果程序位于您的计算机的系统路径 中，或者您将其放在Olex2程序主目录下.已知的程序如下所示：&& ~SADABS~ $file.which(SADABS.exe) ~XP~ $file.which(shelxp.exe) $file.which(xp.exe) ~ShelXS~ $file.which(shelxs.exe) ~XS (Bruker)~ $file.which(xs.exe) ~ShelXL~ $file.which(shelxl.exe) ~XL (Bruker)~ $file.which(xl.exe) && .
setup-title-6 Automatic Updates . . . . . . 自动更新 .
setup-txt-6 Olex2 is under active development. Many new features are constantly added and the whole GUI and workflow design is under constant flux. We therefore recommend to leave the automatic updates switched on. Every time Olex2 starts, it checks on our server whether there are any updates and will proceed to download and install them automatically in the background. Changes will be effective on the next restart. . . . . . . Olex2仍在开发中。很多新的特性将被不断的加入进来，但整个GUI和工作流程设计不会有大的变动。因此，我们建议将自动更新打开。这样每次启动Olex2都将检查我们服务器，如果有更新，则将自动下载和安装。更新后并不需要重新启动Olex2，很多更新都是一些很小的文件。
目前，我们保持两个版本的更新。一个是
http://www.dimas.dur.ac.uk/olex-distro
另一个是
http://www.dimas.dur.ac.uk/olex-distro-test
Test服务器为最新的更新，另一个为大约一个月前的更新。
如果您想改变更新设置，请在程序顶端菜单栏中选择
Help>Update Options
。如果需要的话，您可以在此设置您的proxy settings。 .
setup-title-7 Setup 7 . . . . . . Setup 7 .
setup-txt-7 Setup 7 Txt . . . . . . Setup 7 Txt .
history-help Every step along the process of structure solution and refinement is automatically databased within Olex2 - the 'History'.
Every time a structure is solved, a new history branch is created. Using the drop-down menu, the latest structure stored in the selected branch will automatically be loaded. It is possible to delete and rename branches. . . . . . . 在Olex2中进行的每一步结构解析和精修都被自动保持在数据库中－'历史'。每当解析结构一次，新的历史组将被创建。使用下拉菜单选择历史组后，此次解析的最新的结构将被自动载入。历史组能被命名和删除 .
exclude-hkl-help Conditions for reflections to be excluded can be set here
&&
@Standard Mode (OR)@
This will exclude all reflections where h, k, and l fulfill the conditions you specify independently
@AND Mode@
When the 'AND' tickbox is ticked, the conditions you specify for h, k and l have to be fulfilled simultanesoulsy in the same reflection
&& . . . . . . 在此能选择排除衍射点的条件&&@标准模式 (OR)@这将所有h、k或l能单独符合您指定条件的衍射点排除在外@逻辑和模式@当‘逻辑和’选项框被勾上后，只有h、k和l同时都满足条件的衍射点才被排除在外&& .
reflection-statistics-help Currently there is only the Wilson Plot available here. . . . . . . 目前只能提供Wilson Plot统计图。 .
AFIX-use-help &&
~m = 5~
Regular pentagon
~m = 6~
Regular hexagon
~m = 10~
Idealized pentamethylcyclopentadienyl (Cp*)
~m = 11~
Idealized naphthalene group
~No atoms selected~
Olex2 will automatically search for all occurrences of the selected group in the structure and set the appropriate instructions.
~One Atom Selected~
The selected atom will be set as the pivot atom of a new rigid group.
~More than one atom selected~
Select 5, 6, 10 or 10 atoms respectively for m = 5, 6, 10 or 11 and the selected atoms will form a new rigid group.
&& . . . . . . &&~m = 5~正五边形~m = 6~正六边形~m = 10~理想的五甲基环戊二烯基(Cp*)~m = 11~理想的萘环~没有选择原子~Olex2将自动搜索结构中存在的已选择刚性基团，并加上适当的命令。~已选一个原子~已选的原子将作为新刚性基团的中心原子。~已选多个原子~选择5，6，10或11个原子将分别对应m = 5，6，10或11，并且已选的原子将组成新的刚性基团。&& .
AFIX-help &&~AFIX mn d[#] sof[11] U[10.08]~AFIX applies constraints and/or generates idealized coordinates for all atoms until the next AFIX instruction is read. The digits mn of the AFIX code control two logically quite separate operations. Although this is confusing for new users, it has been retained for upwards compatibility with SHELX-76, and because it provides a very concise notation. m refers to geometrical operations which are performed before the first refinement cycle (hydrogen atoms are idealized before every cycle), and n sets up constraints which are applied throughout the least-squares refinement. n is always a single digit; m may be two, one or zero digits (the last corresponds to m = 0).&&ShelX-97 Manual . . . . . . 英语 .
news-5 Olex2 now has full support for all Shelx AFIX commands. See Tools > Shelx Constraints . . . . Olex2 now has full support for all Shelx AFIX commands. See Tools > Shelx Constraints . Olex2现在能全面支持Shelx所有的AFIX 模式。 详情请见 工具 Shelx Constraints .
news-5-title Full AFIX Support . . . . Volle AFIX Unterstützung . 全面的AFIX支持 .
news-6
»
John Warren's Olex2 xForum
»
Searchable Manual and How-to's
»
Olex2 paper published in J. Appl. Cryst.
»
Bug reports and Frequently Asked Questions . . . . » Ilia Guzei's Olex2 Manual
» Olex2 paper published in J. Appl. Cryst.
» Bug reports and Frequently Asked Questions
» Problems with ATI Radeon graphics cards
. » Ilia Guzei's Olex2 Manual
» Olex2 paper published in J. Appl. Cryst.
» 错误报告和常见问题
» ATI Radeon图形卡问题
.
news-6-title www.olex2.org . . . . . . www.olex2.org .
expand-short-contacts-help &&Move the slider to adjust the threshold for short contacts to be displayed.
Alternatively, you can add the required value in the text box.
Note: the value has to be between 0.9 and 1.7 Angstrom.
Short inter and intramolecular distances will be displayed.
If there are intermolecular interactions within the given threshold,
clicking on these bonds will expand the missing symmetry equivalent part.&& . . . . . . &&移动滑条调节短程相互作用显示的阈值。您也可以将所需要的数值填入文本框内。
注意: 此数值必须在0.9到1.7埃内，这样短程的分子内和分子间距离将显示出来。如果在给定的阈值内有分子间相互作用，请点击那些键以扩展出对称性等同的部分。&& .
edit-atom-help Sometimes you may want to edit your structure using a text-based representation of your current structure model. Olex will generate such a file on request and display it in its own text editor, where you can make changes to the model. The default output format is the ShelX format, because many users are familiar with this representation of a structure model.&&@Edit Atom(s)@If you have no atoms selected, all atoms in your structure will be included, otherwise only those atoms, that are currently selected, will appear in the text. This is particularly useful if you are working on a big structure. Atoms will be shown with all their dependencies: attached hydrogen atoms, constraints and restraints are all displayed in the top of the window. XX editatom XX@Edit Instructions@Shows only the 'instruction' part of the model - these are the instructions that will be taken into account by the refinement engine on the next refinement cycle.XX editins XX&& . . . . . . 有时您可能想用文本编辑模式修改当前结构。因此Olex2会生成类似文件，并通过自带的文本编辑器您可以对模型进行编辑。 默认的输入格式为Shelx格式，因为毕竟大多数用户对此格式很熟悉。&& @编辑原子@ 如果您没有选择原子，那将显示结构中的所有原子，否则仅显示已选原子。 这对精修尤其是精修大型结构有着很大的帮助。 原子的 所有 属性都将显示在窗口的上端，如键联的氢原子，系统规定参数和限制性参数 XX 编辑原子 XX @编辑命令@ 仅显示模型精修的命令部分－这些命令将应用于下一轮的精修中。 XX 编辑INS XX && .
model-disorder-help &&~Split Atoms~Select how you would like to constrain/restrain the atoms in question (or select the blank, if you don't want to constrain/restrain them), then click on those atoms you would like to 'split'. Move the newly 'generated' atoms to where you would like them to be (by holding the SHIFT key while clicking on them).~Move Hydrogen Atoms~This tool can also be used to move Hydrogen atoms to a position inidcated by the presence of residual electron density. Left click on the atom while pressing the SHIFT key - and you can move any atom where you would like it to be. Any constraints and restraints applied to that atom will still apply.When you are done, press the ESC key.&& . . . . . . && 点击此链接，再点击您想‘分裂’的原子。移动新‘生成’的原子到您所认可的位置上（按住Shift键的同时点击要移动的原子）然后进行精修。
此工具也能用于把氢原子移动到有残余电子密度处。在按住Shift键的同时，用鼠标左键点击原子－您能将任何原子移动到您认可的位置上。所有系统规定参数和限制性参数都仍会应用新原子上。 && .
Electron-Density-Peak-Slider-help && ~Electron Density Peak Slider~Move the slider to the left to filter out strongest peaks first, or to the right to filter out weakest peaks first. You can then do things like name $Q C - and this will only apply to the currently visible peaks. The same goes for the Select and Delete buttons.TT 3D_view_tutorial,Electron-Density-Peak-Slider-help TT&& . . . . . . && 移动滑条到左边将先滤除最高的电子云密度残余峰，而将滑条移动到右边能先滤除最低的电子云密度残余峰。然后您可以使用其它功能如‘name $Q C’等。&& .
quick-drawing-style-help &&If one or more atoms are selected, these preset display styles will be applied to the selected atoms. If there is no selection all atoms will be displayed in the new style.&& . . . . . . &&如果一个或多个原子被选定了，那么这些已设定的显示模式将被应用于这些已选原子上。如果没有选择原子，那这些显示模式将应用于所有原子上。&& .
Match-Naming-help If you have a structure with two or more matching moieties, you only need to name one of these. Olex2 will then match this naming scheme to the other molecule.This is important in structures with Z' larger than 1 and also in structures where a metal is coordinated to more than one ligand of the same type. In this case you will need to set the maximum number of bonds for the central metal ion to 0 (right-click, then Bonds).&&Select any one atom of the correctly named molecule, and then select any one atom of the other molecule. Enter a suffix character into the box, then click the link.This will transfer the naming scheme of the first molecule to the second molecule with the suffix letter you have chosen.XX match sel -n=suffix XX
Instead of merely adding a suffix, you can also replace the first character of the original naming scheme with another character. This is useful, for example, if you wish to name all atoms in one ligand like C101, C102, C102 ... and corresponding atoms in the other ligand like C201, C202, C203 ... This is achieved by:XX match sel -n=$suffix XXEqually, the last character of an atom name can be replaced:XX match sel -n=-suffix XXThere is no gui for these replacements, you will have to type the lines above from the command line.&& . . . . . . . .
OlexID English French Arabic Russian Japanese German Spanish Chinese Greek
Quicktools-help This line contains a number of shortcuts to commonly used functions.&&~
~Atom Label~ The atom list will be sorted by atom label alone.
~Atomic Mass~ The atom list will be sorted by atomic mass alone.
~Moiety~ The sorted list (see above) can then be split such that chemical moietiesstay together in blocks.@Sorting by Command Line@
~Atom sort arguments~:
m - atomic weight
l - label, considering numbers
p - part, 0 is first followed by all positive parts in ascending order and then negative ones
h - to treat hydrogen atoms independent of the pivot atom.
~Moiety sort arguments:~s - by size
h - by heaviest atom
m - by molecular weight
~Usage:~
XX sort [+atom_sort_type] XXorXX sort [Atoms] [moiety [+moety sort type] [moiety atoms]] XX
If just 'moiety' is provided - the atoms will be split into the moieties without sorting.
~Example~XX sort +ml F2 F1 moiety +s XX- will sort atoms by atomic weight and label, put F1after F2 and form moieties sorted by size. Note that when sorting atoms, anysubsequent sort type operates inside the groups created by the preceeding sorttypes.TT sorting_tutorial,sorting-help TT&& . . . . . . . .
Quick-Drawing-Styles-help This tool allows you to quickly select from a number of preset drawing styles. If no atoms are selected, then the new style will apply to all atoms, otherwise it will apply only to the current selection.&&~Balls & Sticks~Atoms are shown as spheres. The size of the sphere depends on the radiusof the atom type represented by the sphere.XX pers XX~Ellipsoids~Aniosotropic atoms are shown as ellipsoids. Isotropic atoms are shown as spheres, who'se size depends on the value of the Uiso of the individual atom represented by the sphere.XX telp n XXwhere default n = 50%~Wireframe~The structure is shwon as a wireframeXX proj XX~Sphere Packing~Atoms are represented as space-filling spheresXX sfil XX~Tubes~Atoms are represented as connected tubesXX tubes XX~Default Style~All display settings are reset to the default valuesXX default XX~Polyhedra~Shows the structure in a polyhedral representationXX mask atoms 37 XX && . . . . . . 此工具能快速选择已有的绘图风格。如果没有选定原子，那新的风格将应用与 所有 原子，否则只是应用于当前已选原子。 && ~球棍型~ 原子被显示为球形，球的半径决定于原子种类。 XX pers XX ~椭球型~ 各向异性原子显示为椭球体，各向同性原子仍显示为球形，球体的大小决定于每个原子的Uiso值。 XX telp n XX 默认值为 n = 50% ~线框型~ 用线框型风格显示结构。 XX proj XX ~球型堆积~ 原子显示为球型空间堆积模式。 XX sfil XX ~管型~ 用相连接的管来显示原子。XX tubes XX ~默认风格~ 所有显示风格将被重置为默认值。 XX default XX && .
hydrogen-atoms-target Tools for dealing with Hydrogen Atoms
- Show/Hide Hydrogen Labels
- HIMP equivalent
- Add Hydrogen atoms geometrically
- Automatically place Hydrogen atoms . . . . . . 氢原子处理工具
- 显示/隐藏氢原子标签
- HIMP 等同
- 几何加氢
- 自动摆放氢原子 .
mpln-target Calculate the mean plane of the current selection . . . . Gemittelte Ebene Berechnen . 计算当前所选的平均平面。 .
line-target Calculate a best line through the current selection . . . . Calculate a best line through the current selection . 计算通过当前所选目标的最佳连线。 .
sel-target Print geometric information on the current selection . . . . Geometrische Information der aktuellen Auswahl ausdrucken . 显示当前所选的几何信息。 .
esd-refine-target Executes a refinement, if this is required to obtain esd's of geometric parameters. . . . . Eine Verfeinerung Ausführen, sodass Informationen zu den e.s.d gespeichert werden können . 如果需要获得几何参数的估计标准偏差，请精修一次。 .
esd-target Returns geometric parameters with esd's . . . . Geometrische Parameter mit e.s.d ausdrucken . 返回几何参数及其估计标准偏差。 .
anis-target Make selected atoms anisotropic. If no atoms are selected, all atoms will be transformed . . . . Make selected atoms anisotropic. If no atoms are selected, all atoms will be transformed . 对已选原子做各向异性处理。如果没有选定原子，则所有原子做各向异性处理。 .
disorder-link-selected-help When an atom is found in more than one site in the structure, this atom is said to be disordered. Of course, there is only ONE atom which occupies either one or the other site. So, each of the two sites has an 'occupancy' - a fraction - telling us what statistical percentage of the atom resides in that particular site. Since there is one atom in total, these occupancies need to add up to 1 (or 100%%).&&~Occupancies~Clicking this link will make sure that the occupancies of all atoms in the first half of the selection (in the order in which they were clicked) and all atoms in the second half of the selection add up to 100%.XX fvar sel XX~Parts & Occupancies~Same as above, plus the first half of the selection will be assigned to one 'part' and the second half of the selection to another part. No bonds will be drawn between atoms belonging to different parts. XX part -p=2 lo sel XX&& . . . . . . 当结构中一原子出现在多个位置上，那么此原子被认为是无序。当然，在此是指一个原子出现在这个或那个位置上。 所以，此两个位置上都有一个为分数的占有率参数来说明原子在特定位置上出现的统计学几率。因为这实际上总计为一个原子，所以占有率之和应该为1(或 100%)。 && ~占有率~ 点击此链接能确认所选的前半部分的原子占有率与后半部分原子的占有率之和为100%。 XX fvar sel XX ~组 & 占有率~ 与上述相同，但增加使前半部分所选原子将被指定为一组，而第二部分所选原子将指定为另一组。 在两组不同原子间是不会成键。 XX part -p=2 lo sel XX && .
disorder-link-constraints-help When modelling disorder, it is often a good idea to make sure that the disordered partlially occupied atoms 'behave' in the refinement. It is oftne necessary to apply constraints and/or restraints in the early stages of modelling disorder.&&~EADP~This will do everything that 'Parts & Occupancies' above does, plus the disordered parts will be constraint such that their ADPs will be the same (See l[EADP,EADP,help]).~ISOR~Same as above, except the ADPs will be restraint with l[ISOR,ISOR,help].&& . . . . . . 当模型无序化时，常常需要在精修中确认部分占有的无序原子‘表现行为’。这就有必要在模型无序化的初期阶段加入规定参数和/或限制性参数。 && ~EADP~ 与‘组 & 占有率’相似，增加了将无序组之间的ADP限制相同数值。(参见 l[EADP]). ~ISOR~ 除将ADP用l[ISOR]限制为，与上述相似。 && .
disorder-show-parts-help This tool allows you to show selected parts of of your struture.
&&
~ShowP~
XX showP 0 1 XX Will show part 0 and part 1
XX showP 1 2 XX Will show part 1 and part 2
XX showP XX Will show all parts
&& . . . . . . 此工具按您的选择显示结构的不同组（part）。&& ~ShowP~ XX showP 0 1 XX 将显示第0组和第1组 XX showP 1 2 XX 将显示第1组和第2组 XX showP XX 将显示所有组 && .
calculate-voids-help && ~Calculate Voids~This tool will calculate void space in your structure.XXcalcvoidXX && . . . . . . 此工具将计算结构中的空隙空间。 && @查看@ ~表面~ ~线条~ XX calcvoid XX @等级@ && .
help-target Olex2 keeps track of everything
that happened to your structure.
Here you can go back to a previous state. . . . . . . Olex2会保存在结构上的所有的改变。
在此您可以回到先前的状态。 .
history-target Olex2 keeps track of everything
that happened to your structure.
- Go back to a previous state
- Select a previous solution
- Rename a previous solution tree . . . . . . Olex2会保存在结构上的所有的改变。
在此您可以回到先前的状态。
- 选择先前的解析历史组
- 重命名先前的解析历史组 .
toolbox-target A collection of useful tools.
- Make all peaks Carbon
- Move Atoms
- Show/Hide Peaks
- Expand Short Contacts
- Peak Slider . . . . . . 此为一些很有用的工具集合。
- 所有峰定为碳
- 移动原子
- 显示/隐藏电子云密度峰
- 扩展短程相互作用
- 电子云密度峰滑条 .
select-target Tools for selecting particular atoms
in your structure e.g.:
- Previous Selection
- Invert Selection
- Select Rings . . . . . . 在您的结构中选择特定原子的工具
例如:
- 上一次选择
- 反选
- 选择环 .
sucrose-introduction-tutorial . . . . . . . . .
sucrose-space-group-tutorial . . . . . . . . .
naming-target Tools for naming atoms.
- Choose atom number
- Add suffix to atom name
- Change atom type . . . . . . 原子命名工具。
- 选择原子序号
- 对原子名称加后缀
- 改变原子种类 .
sucrose-solve-tutorial . . . . . . . . .
sucrose-assign-tutorial . . . . . . . . .
sucrose-refine-tutorial . . . . . . . . .
sorting-target Sorts the textual representation of your structure
- By atomic mass and label
- By label
- Splits your list in moieties . . . . . . 整理结构的文本模式显示。
- 按照原子量和元素符号
- 按照元素符号
- 按照不同组 .
quick-drawing-styles-target Quickly access preset drawing styles
- Balls & Sticks
- Ellipsoids
- Wireframe
- Sphere Packing
- Tubes . . . . . . 快速绘图风格
- 球棍型
- 椭球型
- 线框型
- 球型堆积
- 管型 .
geometry-target Obtain measurements on your structure
- Mean Plane
- Best Line
- Distances and Angles
- ESD's . . . . . . 结构中的测量工具
- 平均平面
- 最佳连线
- 距离和角度
- 估计标准偏差 .
olex2-home-target Go to the Olex2 start page . . . . . . 回到OLex2起始页 .
editins-target Edit the instructions for your structure
Only the instructions will be shown,
not the atoms! . . . . . . . .
editatom-target Edit atoms in a textual representation.
- Selected atoms, if any are selected
- All atoms, if none are selected . . . . . . 通过文本模式编辑原子。
- 已选原子（如果已经选择部分原子）
- 所有原子（如果没有选择原子） .
dire-target Open the directory of the current structure.
- or type 'dire' . . . . . . 打开当前结构所在目录。
- 或输入‘dire’ .
consoletext-target Displays the contents of the console in a text editor.
- type 'text' . . . . . . 通过文本编辑器显示控制台的内容。
- 输入‘text’ .
snuminfo-target Expand the information on this structure. . . . . . . 详述当前结构信息。 .
tip-1 t^Selecting Multiple Atoms^tMultiple atoms can be selected by clicking on more than one atom in turn. You can also draw a rectangle around atoms by hoding the Shift-key while dragging the mouse with the left mouse button pressed. . . . . t^Mehrere Atome gleichzeitig anwählen^tKlicken Sie einfach nacheinander auf alle Atome, die sie in ihrer Auswahl haben wollen. Sie können auch mit gedrückter <
Items that do not have a tooltip (yet) will display the command that will be carried out when clicking on them. For example, the link in the fist line of this tip of the day does not have a tooltip - see what happens when you hover over it!XX html.Tooltips {True/False} XXIf no argument is supplied, tooltips will be toggled. . . . . . . t^工具提示^t 点击 此处 打开工具提示。您可以在‘设置’中关闭工具提示。
没有工具提示的项目将在点击时显示所执行的命令。例如，在每天提示的第一行链接是没有工具提示的。－把鼠标停留在链接上后，请观察变化！ XX html.Tooltips {True/False} XX 如果没有提供参数，工具提示将被关闭。 .
tip-4 t^Lines of Text^tThe number of lines of text in the main window can be controlledXX lines 5 XXThis will show 5 lines of text in the main window. If you want to see all lines, typeXX lines -1 XXIt is also possible to hide the structure and the text in turn with <
To Rotate the Structure around an axis perpendicular to the screen, hold down the Ctrl Key while moving the mouse on the background with the left-mouse button pressed.
t^To zoom the structure^t, keep the right mouse button pressed anywhere on the background and move the mouse. . . . . . . t^旋转结构^t 在主窗口 背景 的任何位置按住鼠标左键不放，再移动鼠标即可在屏幕内旋转结构。(注意: 如果是左键点击原子或键将为选择功能，并不会旋转结构)
如果要围绕 垂直于屏幕 的轴旋转结构，请按住Ctrl键并同时在背景处按住鼠标左键，然后移动鼠标即可。
t^在背景任何位置按住鼠标右键，并移动鼠标即可缩放结构视图。 .
tip-6 t^Backgrounds^tThe background of the structure window can be customised in the following ways:
F4 will toggle the graduated background on and off. The colour of this background can be set by:XX grad XXF2 will switch between white and a coloured background. To set the colour of the background (as well as many other settings): right-click on the background > Draw Styles > Scene Settings. . . . . . . t^背景^t 结构显示窗口的背景可以通过如下方法进行定制
按F4将开关梯度背景显示。此时背景颜色通过: XX grad XX设置。按F2将切换白色和彩色背景。设置背景颜色(和其它设置一样): 在背景处点击右键 > 绘画风格 > 背景设置。 .
sort_ml-msg Atom list is now sorted by atomic mass and atom labels. . . . . Atome sind nun nach Masse und Namen sortiert. . 现在原子按照原子量和元素符号分类排序。 .
sort_l-msg Atom list is now sorted alphanumerically by labels . . . . . . 现在原子按照原子标签字母排序。 .
sort_m-msg Atom list is now sorted by the atomic mass. . . . . . . 现在原子按照原子量排序。 .
sort_moiety-msg The sorted list has been arranged such that atoms belonging to the same moiety staty together. . . . . . . 列表同一组中的原子被整理在一起。 .
rotate-target Rotate your structure on the screen
- align along unit cell axes
- rotate by a certain amount in degrees
- continuously rotate the structure . . . . . . 在屏幕上旋转结构
- 沿着晶轴方向
- 一定角度的旋转
- 连续旋转结构 .
show-target Select items to show or hide on the screen:
- unit cell
- basis vector
- hydrogen atoms/labels
. . . . . . 显示/隐藏以下项目:
- 晶胞
- 晶轴向量
- 氢原子/标签
.
symmetry-generation-target Tools for generating symmetry equivalent atoms:
- pack
- grow
- copy fragments
- move fragments . . . . . . 此工具可生成对称性等同的原子:
- 堆积k
- 生长
- 复制片段
- 移动片段 .
chemical-tools-target Miscellaneous tools:
- CHN Analysis values for current structure
- Molecular Isotope Patterns
- Molecular Volume
- Polyhedral Volume around atoms . . . . . . 杂项工具:
- 当前结构的元素组成分析
- 分子同位素图谱
-分子体积
- 原子周围多面体体积。 .
OLEX2-conres-target New Olex2 Constraints and Restraints . . . . . . 新的Olex2参数和限制性参数。 .
SHELX-compatible-constraints-target All constraints available with SHELX
- AFIX
- EADP
- EXYZ . . . . . . Shlex提供的所有规定参数
- AFIX
- EADP
- EXYZ .
SHELX-compatible-restraints-target All Restraints available from SHELX
. . . . . . Shelx提供的所有限制性参数
.
disorder-target Tools for dealing with disorder:
- Link atoms
- Link occupancies
- Assign parts
- Show selected parts . . . . . . 此工具主要用来处理无序结构:
- 连接原子
- 连接占有率
- 指定组
- 显示已选组 .
calculate-voids-target Calculate the Voids in your structure . . . . . . 计算结构中的空间。 .
electron-density-target Interactively display the Electron Density
- adjust drawing style
- change atom types and recalculate map
- change resolution . . . . . . 互交式显示电子云密度
- 调节绘制模式
- 改变原子种类和重新计算电子云密度图
- 改变分辨率 .
twinning-target Search for possible twin laws in your structure . . . . . . 在结构中搜寻可能存在的孪晶规则。 .
settings-target Set preferences for Olex2 . . . . . . 设定Olex2参数。 .
overlay-target Overlay and match structures
- Import another structure
- Match fragments (Z' > 1)
- Match substructures . . . . . . 覆盖和匹配结构
- 导入另一个结构
- 匹配片段 (Z' > 1)
- 匹配子结构 .
recent-files-target List files that have recently been opened in Olex2 . . . . . . 列出最近用Olex2打开的文件。 .
refinement-indicators-target See how your refinement is going! . . . . . . 请看您做的精修是如何进行的！ .
bad-reflections-target Examine reflections that do not fit very well
- Omit bad reflections
- Omit occurances of reflections
- Omit reflections by h,k,l . . . . . . . .
reflection-statistics-target Examine your reflection statistics graphically:
- Wilson Plot . . . . . . 通过统计图表检查衍射点:
- Wilson Plot .
electron-density-peaks-target Examine residual electron denisity peaks graphically
- See the relative height of the peaks
- Modify transperancy of peak display . . . . . . 通过图形检查电子云密度残余峰
- 查看相关电子云残余峰高度
- 修改电子云密度残余峰显示 .
start-target Start here!
- Sample Structures
- Open Exising File . . . . . . 在此开始!
- 示例结构
- 打开已有文件 .
news-target Check here for:
- Important announcements
- Tip of the day
- Links to the Olex2 portal . . . . . . 查看此处:
- 重要的公告
- 每天提示
- 连接Olex2网站 .
tip-7 t^Custom Report Styles^tIt is possible to create a custom style for Olex2 reports by making use of Cascading Style Sheets (css). Create a custom css file by editing and renaming this file and this will then appear as an option in the Report > Report Style drop-down box in the GUI. All css items defined in the custom css file will override or extend those defined in thesis.css. . . . . . . t^自定义报告模式^t 现在可能用层叠式样式表（css）生成自定义的Olex2报告模式。修改和重命名 file 可生成自定义的css文件。并且此文件将出现在Report > Report Style的下拉菜单中。所有在自定css文件中规定的css项将覆盖或扩展在thesis.css中的相应部分。 .
tip-8 t^Change Spacegroup P1 to P-1^tFirst, identify two atoms related by the center of inversion and select them.
XX echo ccrd(sel) XXto get the coordinate of the point between the selected atoms. Olex2 will print the fractional coordinates of the center of inversion as 'x,y,z'.
XX push -x, -y, -z XXto move the content of the asymmetric unit so that the center of inversion now is at (0,0,0).
XX changesg P-1 XXto change the space group. Olex2 will try to remove the symmetry related atoms, however if the atoms do not overlap within some vlaue, they have to be removed manually.
Sometimes the molecule looks 'broken' after this operation and the command 'compaq -a' has to be typed to assemble the molecule. . . . . . . . .
sucrose_introduction-tutorial {{
author:Horst,
next:sucrose_space-group,
previous:sucrose_introduction
}}
In this tutorial, you will determine the molecular structure of sucrose. The reflection
data required to do so are included in this distribution of Olex2.
&&
~Load Reflections~
In order to solve a structure, you will need a reflection file (either a raw or a
processed hkl file will do) and a file containing the unit cell dimension and some
other necessary data.
XX reap DataDir()/samples/sucrose/sucrose.hkl XX
To do this action, either type the above line exactly (click
on the main window and start typing!) or click on the link above.
n^The function call DataDir() returns the path to the directory, where
Olex2 stores the information of a particular user. Other built-in functions include
BaseDir() (Olex2 installation directory),
FilePath() (Path to the current structure) and
FileName() (Name of the current structure). In order to see these values, type:
XX echo BaseDir() XX ^n
Since there we also supply a finished model of the sucrose molecule, this has
automatically loaded and you should now see the sucrose molecule on the screen. Of
course, if you have played with this structure before, the model on the screen will
be exactly at the stage where you left it!
The next step would normally be the
l[Space Group Determination,sucrose_space-group,tutorial],
but you may want to skip this part and jump straight to
l[Structure Solution,sucrose_solve,tutorial].
~Contents~
l[Space Group Determination,sucrose_space-group,tutorial]
l[Structure Solution,sucrose_solve,tutorial]
l[Atom Type Assignment,sucrose_assign,tutorial]
l[Structure Refinement,sucrose_refine,tutorial]
&& . . . . . . . .
sucrose_space-group-tutorial {{author:Horst,next:sucrose_solve,previous:sucrose_introduction}}&&~Space Group Determination~The space group of your structure may or may not have been determined by an external program like XPREP. If it has been determined, there will have been a ShelX ins file, which Olex2 would have automatically read and the space group would be taken from the symmetry instructions in that file.The space group can also be determined by Olex2 by issuing the commandXX sg XXThe textual output of this command will have appeared on the screen. If you wish to examine this more carefully, typeXX text XXIf you are unsure as to whether your structure is centrosymmetric or not, it might be a good idea to have a look at the Wilson Plot. XX wilson_plot XXThe little diagram at the bottom of this graph clearly shows that this structure is non-centrosymmetric, and therefore the correct space group must be P21. We can now reset the structure in the correct space group by typingXX reset -s=P21 XXl[Stucture Solution,sucrose_solve,tutorial]&& . . . . . . . .
sucrose_solve-tutorial ** structure **{{author:Horst,next:sucrose_assign,previous:sucrose_space-group}}Structure Solution refers to the part of the structure determination where a list of electron density peaks is obtained from the reflection file.&&~Solution Programs~ There are various programs available that will do this job. Olex2 currently supports ShelXS, ShelXM and it's own structure solution program: smtbx-solve.
You can examine the available programs by clicking on the tab gui[Work,itemstate * 0 tab* 2 tab-work 1 logo1 1 index-work* 1 info-title 1,none]. There you will find three more tabs: Solve, Refine and Report. Right next to the word 'solve' will be a small triangle. If you gui[click,itemstate cbtn* 1 cbtn-refine 2 *settings 0 refine-settings 1>>updatehtml,none] on that, you get access to the settings of the structure solution. The available structure solution programs can be inspected in the drop-down menu 'Solution Programs'n^If you have ShelX installed on your system, but neither ShelXS nor ShelXM appear in the list, you can try to copy the executables into the Olex2 installation directory. It could also be that you are using executables that came with an installation of WinGX - these will not work with Olex2. In this case you will have to contact George Sheldrick directly to obatain new executables - which is of course what you would have to do if you don't have ShelX.^n~Solution Settings~ Each of thesese solution programs has a variety of settings. Depending on the program chosen, these settings can all be adjusted from the Olex2 GUI. If you press the 'Solution Settings Extra' button, you can see and adjust all parameters that are available for the chosen solution program and solution method combination.~Solve the Structure~In the case of our sucrose structure, choose ShelXS as the solution program, and Direct Methods as the solution method. To solve the structure, either click on the 'Solve' button, or type:XX solve XXYou should now see brown spheres, representing electron denisty peaks, on the screen. The spheres vary in transparency, the more transparent they are, the smaller the peak. You should be able to clearly see the sucrose molecule already!
In the next step you will assign these electron density peaks to the correct atom types.
l[Assign Atom Types,sucrose_assign,tutorial]&& . . . . . . . .
sucrose_assign-tutorial {{author:Horst,previous:sucrose_solve,next:sucrose_refine}}We now need to assing these electron density peaks (displayed as brown spheres) to some real atom types. Luckily the sucrose molecule is already visible, so the job is easy.&&~Tidy the Peaks~The fist step is to tidy up some of these peaks so that we can see almost nothing but the actual sucrose molecule. A good tool to use here is the gui[Electron Density Peak Slider,itemstate * 0 tab* 2 tab-work 1 logo1 1 index-work* 1 info-title 1>>itemstate work-toolbox 1,none]. , which can be found under the Toolbox Work tool and should be visible right now. If you move the slider to the left, strong peaks will be deleted first, and if you slide it to the right, weak peaks will be eliminated. Please move the slider to the right now, until all visible electron density peaks in the display correspond to a real atom (about 80 in the box next to the slider).XX showQ 80 XX~Convert all peaks to Carbon~In simple stuctures like this, it is often a good idea to convert all electron denisty peaks to carbon atoms as a starting point. To do so, you can press the 'QC' button (in the first line of Toolbox Work) or issue this commandXX name $q c XX~Refine the Stucture~You now have a model of your structure that conists entirely of carbon atoms. This is of course not the correct structure of sucrose. In order to find out how well our atom assignment matches reality, we need to refine the structure against our reflection data. To do so, press the 'Refine' button or type:XX refine XXThe refinement part is at the heart of crystal structure analysis. The next part of this tutorial will deal with structure refinement.
l[Structure Refinement,sucrose_refine,tutorial]&& . . . . . . . .
sucrose_refine-tutorial {{author:Horst,next:sucrose_introduction,previous:sucrose_assign}}Structure refinement lies at the heart of a crystal structure analysis. It is the step in the analysis where our model (i.e. the assignment of atom types) conforms to the measured reflection data.&&~Refine~To start a refinement with current settings (which will be the default settings unless you have modfied them), either press the 'Refine' button, press Ctrl+r or typeXX refine XXYou can change the refinement settings under the 'Refine' tab by clicking on the little arrow next to the word 'refine'. The available refinement programs should be visible under the 'Refinement Program' dropdown menu, and for each program there will be one or more 'Refinement Options'. You can also set the number of refinement cycles and the number of electron density peaks you wish to see after the refinement. n^These latter two parameters can also be set from the command line by, for example:XX refine 4 20 XXThis will start the refinement with a maximum of 4 cycles and ask for 20 electron density peaks.^n~Examine the Model~Regardless of the refinement program or method used, the spheres representing the carbon atoms in the refined model are not all of the same size. In fact, you should see two lots of sizes: smaller spheres and larger spheres. The size of the spheres represents the a parameter resulting from refinement that tells us how well the current assignment corresponds to reality. If a sphere is too big', the real atom type is lighter than the currently assigned atom type. Conversely, if it is 'too small', the real atom type is heavier. In the case of this structure it is very easy to see which atoms should really be heavier!
At this point, the residual electron denisty peaks (brown spheres) can get into the way. You can toggle their display by pressing Ctrl+q repeatedly and see what happens to them on the screen. You might want to continue with the electron denisty peaks hidden from view.~Re-assign Atoms~There are many ways to re-assign an atom type. Please try all of the following:
- Right-click on one of the small spheres and select Type|O
- Click on two other small spheres in turn, then right-click on one of them Type|O
- Click on yet another one, then click on the button 'O'
- Click on two small spheres, then type:XX name sel O XX- Click on the button 'O', then click on the remaining 'small' spheres in turn.&& . . . . . . . .
center_on_cell_target Center the structure on the unit cell . . . . . . 将结构中心放置在晶胞内 .
center_on_largest_part-target Center the structure on the largest fragment . . . . . . 将结构中心放在最大片段 .
fuse-target Reload the asymmetric unit of the structure . . . . . . 重新载入结构的非对称单元 .
matr_1-target Align view along the a axis . . . . . . 沿a轴方向查看 .
matr_2-target Align view along the b axis . . . . . . 沿b轴方向查看 .
matr_3-target Align view along the c axis . . . . . . 沿c轴方向查看 .
pack_cell-target Generate symmetry equivalent atoms to fill the unit cell . . . . . . 生成晶胞内所有对称性等同的原子 .
pack_limits-target Generate symmetry equivalent atoms within the entered limits . . . . . . 在输入的范围内生成对称性等同的原子 .
a-target Align view along the unit cell a axis . . . . . . 沿晶胞的a轴方向查看 .
b-target Align view along the unit cell b axis . . . . . . 沿晶胞的b轴方向查看 .
c-target Align view along the unit cell c axis . . . . . . 沿晶胞的c轴方向查看 .
x-target Rotate around the x axis of current view . . . . . . 围绕当前视角中x轴旋转 .
y-target Rotate around the y axis of current view . . . . . . 围绕当前视角中y轴旋转 .
z-target Rotate around the z axis of current view . . . . . . 围绕当前视角中z轴旋转 .
atom_label-target Sort atom list alphanumerically by atom label . . . . . . 按照原子标签字母顺序排序 .
mass_&_label-target Sort atom list by atomic mass and label string . . . . . . 按照原子量和标签排序 .
atomic_mass-target Sort atom list by atomic mass . . . . . . 按照原子量排序 .
moieties-target Split atom list into moieties . . . . . . 将原子列表分为两组 .
balls_&_sticks-target Display atoms as ball and stick . . . . . . 显示结构为球棍式 .
wireframe-target Dislplay the stucture in wireframe view . . . . . . 显示结构为线框式 .
sphere_packing-target Show a space-filling representation of the structure . . . . . . 显示结构的空间占有示意图 .
tubes-target Represent the structure as tubes . . . . . . 显示结构为管式 .
default_style-target Load the Olex2 default viewing style . . . . . . 载入Olex2默认显示风格 .
polyhedra-target Show the structre in a polyhedral representation . . . . . . 显示结构为多面体模型 .
symmetry-generation-help This is a collection of tools for creating symmetry equivalent atoms in a structure. &&~Moving and Copying~Sometimes fragments of a structure appear in the 'wrong' place. For example, a counter-ion might be displayed away from a metal complex, or a water molecule of solvation does not appear on the 'correct' side of the main fragment.
With the 'Move Near' and 'Copy Near' modes the structure can be re-assembled in a more suitable way. To do this, you need to do the following:
1. Select the atom of the main fragment that you wish to move subsequently clicked atoms close to.
2. Click on 'Move Near' (to move subsequently clicked atoms) or 'Copy Near' (to create additional symmetry equivalent fragments).
3. While in this mode, any atom clicked, will be moved (or copied) as close to the originally selected atom as possible.XX mode move sel XXXX move sel -c XX&& . . . . . . 这是生成结构中对称性等同原子的工具集合。&& ~移动和复制~ 有时结构中的一些片段出现在‘错误’的位置。例如，相反离子远离金属配合物，或溶剂水分子没有在主片段的‘正确’方位。
利用‘移动至’和‘复制至’模式使得结构以更合适的方式重新组装。在做之前，您需要先做如下步骤:
1. 选择主片段上一个原子，接下来您将选择移动的其它原子到此原子附近。
2. 点击‘移动至’(移动下一步选择的原子)或‘复制至’(将生成另一个对称性等同片段)。
3. 在此模式下，任何点击任何原子都将尽可能移动(或复制)到离第一步所选原子最近的位置上。 XX mode move sel XX XX move sel -c XX && .
tip-9 t^Set maximum number of bonds for an atom^tIt is possible to set a maximum number of bonds to display for a specific atom. Right-click on the atom -> Bonds -> {select value}. Alternatively: Select the atom and then type:XX conn 3 XXwhich will show at most three bonds to the selected atom. Of course you could also provide a specific atom name instead of selecting an atom, e.g.:XX conn C7 3 XXIt is also possible to select the maximum number of bonds to show for all atoms of the same type:XX conn $Ca 6 XXThis will not over-write values that might have been set previously for a specific atom. n^If a positive number is provided, the longest bond(s) will be removed, if a negative number is provided, the shortest bonds will be removed.^n . . . . . . t^设置原子的最大成键数目^t
可以为特殊的原子设定最大的成键数目:右键点击原子 -> Bonds -> {选择数目}，也可以通过选择一个原子然后输入: XX conn 3 XX 来实现，即将显示最多三个与已选原子相连的键。当然，您也可以用特殊原子具体的标签来代替选择原子，例如: XX conn C7 3 XX 。 还能显示所有同类原子的最大成键数目: XX conn $Ca 6 XX ，并且不会覆盖已设定好的特殊原子成键数目。n^如果给出的是一个正值，那么 最长 的键将被删除，如果给出的负值，最短 的键将被删除。^n .
tip-10 t^Set occupancy for atoms^tOccupancies for atoms can be set by Right-click -> Occupancy -> {select value}. This will fix the occupancy to the chosen value. Alternatively, select the atom and typeXX fix occu 0.5 XXThis will fix the occupancy to 0.5.n^It is possible to toggle between a fixed occupancy and a freely refined occupancy by repeating the above steps in the gui (and then select 'free' or 'fixed' from the menu. Alternatively, select the atom and type:XX free occu XX^n . . . . . . t^设定原子占有率^t 通过右键 -> Occupancy -> {选择数值}来设定原子的占有率。这样设定后原子的占有率将被固定为设定值。当然，也可在选择原子后输入: XX fix occu 0.5 XX 命令，即将原子的占有率固定为0.5。n^在上述设定占有率的界面中可以通过选择‘free’或‘fixed’来切换是否精修占有率，也可以在选择原子后输入: XX free occu XX 来设定。^n .
tip-11 t^Adding Hydrogen Atoms^tOlex2 will place hydrogen atoms and constrain them automatically. If you want to place all hydrogen atoms, click on the 'HADD' button under the work tab or simply type:XX hadd XXIf no atoms are selected, hydrogen atoms will be added to all 'suitable' atoms, if there is a selection, only the selected atoms will be included.
It is also possible to generate specific constraints for geometrically generated hydrogen atoms, e.g.:XX hadd 23 XXwill only place hydrogen atoms to atoms with suitable geometry (2 H on sp3). As before, if there is no selection, all atoms wil be considered, otherwise only the selected atoms. This means that, for example, one hydroxy hydrogen can be constraint with AFIX 83 while another one can use AFIX 147. Custom constraints will overwrite constraints placed automatically.n^Olex2 uses the ShelX 'AFIX nm' syntax when dealing with hydrogen constraints.^n . . . . . . t^加氢^t Olex2可以自动加氢并且限制其位置。如果您想加上所有氢原子，请点击在‘工作’界面下的‘AddH’按钮或输入: XX hadd XX 。如果没有选定原子，那么将对所有‘适合’的原子加氢；如果选定了一个或多个原子，则只是对已选原子加氢
加氢会对生成的氢原子产生几何上的限制性参数，例如: XX hadd 23 XX 只会将氢原子放在几何上适当的位置 (2 H on sp3)。同样，如果没有选择原子则将考虑所有原子，否则只是对已选原子加氢。这意味着，一个氢原子可以用AFIX 83限定，而另一个则可以是通过AFIX 147限定。自定义限制性参数将自动覆盖自动定义的限制性参数。 n^Olex2使用ShelX中 'AFIX nm' 规则来处理氢原子的限制性参数。^n .
getting-started_main-window-tutorial **selected,rotated,zoomed,console,background**{{author:Horst,next:getting-started_control-panel,previous:getting-started_main-window}}Now that you have successfully installed Olex2 on your system, it is time to get familiar with Olex2.&&~The Main Window~ is the big window where your molecule is displayed. On startup, Olex2 will load the last structure - and if Olex2 is run for the first time, it will load one of our sample structures, which is shipped with Olex2.The displayed molecule can be rotated (left-click somewhere on the background) and zoomed (right-click on the background, then move the mouse).
Atoms and bonds of your molecule can be selected (left-click on them), some of their properties can be viewed (hover the mouse over them), and some of their properties can be changed (right-click on them).
The main window also doubles up as the Olex2 console: Whenever you start typing, text will appear in the bottom left hand corner of the main window. If you press <
The displayed molecule can be rotated (left-click somewhere on the background) and zoomed (right-click on the background, then move the mouse).
Atoms and bonds of your molecule can be selected (left-click on them), some of their properties can be viewed (hover the mouse over them), and some of their properties can be changed (right-click on them).
The main window also doubles up as the Olex2 console: Whenever you start typing, text will appear in the bottom left hand corner of the main window. If you press <
Tools are loosely arranged according to one of the four categories: work, view, tools and info. Of course it is not always possible to find the just one best place for any given tool - please let us know if you think a particular tool is misplaced!~The Menu Bar~ is the bar at the top of the Olex2 window. This bar has been neglected by us for a while and does, at the moment, not reflect the full potential of Olex2. Please bear with us until this is fixed!~The Context Menu~ is whatever you get when you right-click on any object in the main window of Olex2. This menu changes depending on what you click - so go ahead and play around with it!&& . . . . . . . .
tip-12 t^Selecting Atoms that are 'too small'^tBy default, Olex2 displays atoms and their thermal parameters. Anisiotropically refined atoms will be represented with their thermal ellipsoids. Atoms, that have been refined isotropically will shown as spheres, where the radius represents the Ueq value of the atom. If this value becomes very small, the sphere will be very small - and often too small to be selected by the mouse. In this case you will need to draw a rectangle around the atom you wish to select (press the <
t^Move^tXX mode move -c XXonce a fragment atom is selected this mode will copy any other fragment (which is clicked) as close to the selected atom as possible . . . . . . . .
Wilson Plot cctbx Wilson Plot (cctbx) . . . . Wilson Graph (cctbx) . Wilson Plot cctbx .
Systematic Absences Systematic Absences . . . . Systematische Abwesenheit . 系统消光 .
Wilson Plot Olex2 Wilson Plot (Olex2) . . . . Wilson Graph (Olex2) . Wilson Plot Olex2 .
Cumulative Cumulative . . . . Kumulativ . Cumulative .
Reflection Statistics Reflection Statistics . . . . Reflexstatistik . 衍射数据统计 .
AND AND . . . . UND . . .
Exclude Exclude . . . . Auschliessen . . .
Show Cumulative Intensities Show Cumulative Intensities . . . . Kumulative Intensitäten zeigen . . .
Changing Language to Changing Language to . . . . Ändere die Sprache nach . . .
Please wait while uploading your changes Please Wait while uploading your changes. . . . . Bitte warten sie, bis ihre Änerungen in der Datenbank gespeichert sind. . . .
Make Graph Make Graph . . . . Graph erstellen . 作图 .
Q Peak Intensities Q Peak Intensities . . . . Q-Peak Intnsitäten . Q峰强度 .
AFIX Commands AFIX Commands . . . . AFIX Befehle . AFIX命令 .
Variables Variables . . . . Variablen . 变量 .
Rename Rename . . . . Umbenennen . 重命名 .
Name Name Name . . . Benennen . 名称 .
Close sorting Close sorting . . . . Sortierung schliessen . . .
Default Style Default Style . . . . Default Stil . 默认风格 .
Ellipsoids|H Ellipsoids|H . . . . Ellipsoide|H . 椭球模型|H .
Low Quality Low Quality . . . . Niedrige Qual . 低质量图形 .
Pack Cell Pack Cell . . . . Zelle Packen . 晶胞中的堆积图 .
Pack Limits Pack to limits . . . . Packen . 堆积图 .
Show Basis Show Basis . . . . Basis zeigen . 显示晶轴矢量 .
Show Cell Show Cell . . . . Zelle zeigen . 显示晶胞 .
Shelx Compatible Constraints Shelx Compatible Constraints . . . . . . Shelx限制性精修 .
Constraint Constraint . . . . . . 限制性精修命令 .
Olex2 Constraints And Restraints Olex2 Constraints And Restraints . . . . . . Olex2 规定参数和限制性精修 .
tip-16 t^Hiding Atoms and Fragments^t&&~Selected Atoms and Bonds~Any graphical object in Olex2 can be hidden from view. Right-click on the selection then Graphics>Hide will achive this.~Hide a whole Fragment~
If your structure has more than one fragments, you can hide a particular fragment with Right-click and then Fragment>Hide. Other options are available there, please play with them for a bit!~Hide the whole Structure~ <
For more information see:
E.R. Howells, D.C. Phillips and D. Rogers, Acta Cryst. (1950). 3, 210-214. XX cumulative_intensity XX && . . . . . . . .
fobs-vs-fcalc-help && ~Fobs vs Fcalc~ This plots the observed amplitudes against the calculated amplitudes. If the model is a good fit for the data, the data points should form a straight line with gradient equal to one and intercept at the origin. Reflections that have been omitted (either individually or by angle cutoff) are also shown on the graph, but not included in the calculation of the line of best fit. XX fobs_fcalc XX && . . . . . . . .
wilson-plot-help && ~Wilson Plot~ For more information see:
Giacovazzo et al., (2002). Fundamentals of Crystallography, 2nd ed. Oxford: Oxford Science Publications. XX wilson_plot XX && . . . . . . . .
completeness-plot-help && ~Completeness Plot~ The merged data are sorted into bins by resolution, and the percentage completeness for each bin is calculated. A list of missing data is shown. XX completeness XX && . . . . . . . .
Toolbar-Model-help This is a collection of three basic tools needed for model building.&&~Assign Atom Types~All atom types that are currently in your formula are represented as a small button. You can click on one of these buttons and will go into an atom type assignment mode for this particular atom type. Atoms you click subsequently will become that atom type. Alternatively, you can make a selection of atoms first, and then click the atom type symbol. The buttons will appear red, if there are fewer atoms of that type in your model compared to the formula you have initially given. They turn green if the numbers do agree.XX name sel C XXXX mode name C XX~Geometrically Place Hydrogen Atoms~Pressing this button will cause Olex2 to place hydrogen atoms geometrically. If there is no selection of atoms, hydrogen atoms will be placed where possible. If there is a selection, they will only be added to the selected atoms.XX Hadd XX~Toggle Isotropic/Anisotropic~With these buttons, you can make atoms either isotropic or anisotropic. If there is no selection this will apply to all atoms; if there is a selection, then this change will only apply to the selection.XX isot XXXX anis XXn^If the tickbox is ticked, then refinement will happen automatically after changing either isot/anis or hadd.^n TT 3D_view_tutorial,Toolbar-Model-help TT && . . . . . . . .
rename-history-help You can rename any of the automatically generated histories. Click on the 'Rename' button and then type the new name directly in the drop-down box. . . . . . . . .
labels-help You can select what you would like to see as labels in the molecule display. If a particular property is not applicable for a particular atom, there will be no label. && ~Atom Names~All atom names of non-hydrogen atoms will be displayed next to the atoms. XX labels -l XX ~Occupancy~The occupancies will be displayed for all atoms where the occupancy is not 1. XX labels -o XX~Parts~If an atom belongs to a particular part, the part number will be shown. XX labels -p XX~Link Codes~If atoms are linked, the link code will be shown XX labels -lo XX && . . . . . . . .
reflection-file-help Olex2 will manage the reflection file against which you want to refine your model. Select the file from the drop-down menu and this is the file that will be used. . . . . . . . .
Automatic-Hydrogen-Naming-help Olex2 will keep track of the naming of hydrogen atoms automatically. This feature can be switched off by unticking the 'Automatic Hydrogen Naming' box. . . . . . . . .
Growing-help By default, Olex2 shows the asymmetric unit only. Line before a Table. &&~Mode Grow~will show clickable 'bonds' which will expand symmetry equivalent parts. XX mode grow XXThere are various modifiers for this command: ~Short Contacts~will show these growable 'bonds' to those atoms where 'short interactions' exist XX mode grow -s XX ~Selection~will show growable 'bonds' to other occurances of the currently selected atoms XX mode grow -r XX ~Van der Waals Radii~will show growable 'bonds' to other occurances of the currently selected atoms that are at least the indicated distance away from the selected atom. XX mode grow -v 2.0 XX TTgrow_tutorial,Growing-helpTT && . . . . . . . .
show-parts-help If your structure contains atoms that have been assigned to parts, then it is sometimes useful to look only at atoms belonging to the same part.XX showP 1 XXWill show only atoms belonging to Part 1XX showP 0 2 XXWill only show atoms that don't belong to a Part and those that belong to Part 1.XX showP 0 XXWill show all atoms. . . . . . . . .
Calculate-Bounding-Box-help A rectangular bounding box is calculated for your molecule and displayed on the screen.XX wbox XX . . . . . . . .
Calculate-Polyhedral-Volume-help Calculates the polyhedral volume of a polyheder that is defined by the selected atom.XX calcvol XX . . . . . . . .
Calculate-Molecular-Volume-help Calculates the Molecular VolumeXX vvol() XX . . . . . . . .
Calculate-Molecular-Isotope-Pattern-help Simulates a molecular isotope pattern for your structureXX calcms XX . . . . . . . .
Calculate-CHN-Analysis-help Calculates the expected values of a CHN analysis from your structure model XX calcCHN() XX . . . . . . . .
Link-Selected-help TWO Selected atoms will be 'linked' in the refinement.&&~Occupancies~The occupancies will be linked such that the individual occupancies add up to unity.XX fvar sel XX~Parts and Occupancies~XX part -p=2 -lo sel XXThe occupancies will be linked such that the individual occupancies add up to unity and the selected atoms will be added to Parts.n^the -p parameter determines the number of parts that should be assigned. -lo stands for 'link occupancy.^n&& . . . . . . . .
normal-probability-plot-help && ~Normal Probability Plot~ The normal probability plot is a graphical technique for assessing whether or not a data set is approximately normally distributed. The weighted residuals are sorted by order of magnitude, and plotted against the values expected for a theoretical normal distribution. An ideal normal probability plot will be linear, with a gradient of 1 and passing through the origin. Large deviations from this can indicate deficiencies with the model, weights and scaling respectively. XX normal_probability XX && . . . . . . . .
fobs/fcalc-vs-resolution-help && ~Fobs/Fcalc vs resolution~ This graph shows the variation of the Fobs/Fcalc ratio with resolution. If the model is a good match for the data, then most of the points should be close to the line indicating an Fobs/Fcalc ratio of 1. Deviations from this may indicate systematic errors in the data with respect to resolution. XX fobs_over_fcalc XX && . . . . . . . .
Fill the Unit Cell Fill Unit Cell . . . . . . Fill the Unit Cell .
Short Short . . . . Kurz . Short .
VdW VdW . . . . VdW . VdW .
center_on-target Centre the structure on the selected atom or the centroid of the selected atoms. . . . . . . . .
images_add_labels_to_atoms Add labels to the selected atoms Add labels to the selected atoms . . . . . . .
images_add_labels_to_non_H_atoms to non H atoms to non H atoms . . . Nicht H Atome beschriften . . .
images_move_labels Move the labels with the left mouse while holding down the SHIFT key Move the labels with the left mouse while holding down the SHIFT key . . . . . . .
images_labels_tip Tip: When labels are active, CTRL+A will select ALL labels. Selected labels can be moved while the SHIFT key is pressed and can also be deleted by pressing the delete key. Tip: When labels are active, CTRL+A will select ALL labels. Selected labels can be moved while the SHIFT key is pressed and can also be deleted by pressing the delete key. . . . . . . .
images_label_colour Choose the label colour Choose the label colour . . . . . . .
images_label_box Label Box Label Box . . . Beschriftungsbox . . .
images_transparent_box Transparent Box Transparent Box . . . Durchsichtige Box . . .
images_octant_line_width Octant Line Width Octant Line Width . . . . . . .
Lines Lines Lines . . . Linien . . .
Bonds Bonds Bonds . . . Bindungen . . .
images_bmp_label_olex_font Choose Label Font (Olex2) Choose Label Font (Olex2) . . . Beschriftungsfong(Olex2) . . .
images_bmp_label_system_font Choose Label Font (System) Choose Label Font (System) . . . Beschriftungsfont (System) . . .
Atoms Atoms Atoms . . . Atome . . .
Font Font Font . . . Font . . .
Octant Octant Octant . . . Oktant . . .
images_dividing_line_width Dividing Line Width Dividing Line Width . . . Teilstrichdicke . . .
images_bond_width Bond Width Bond Width . . . Binungsdicke . . .
images_outline_line_width Outline Line Width Outline Line Width . . . . . . .
images_font_weight Weight (vis. in file) Weight (vis. in file) . . . . . . .
images_H_atom_bonds H Atom Bonds H Atom Bonds . . . H Bindungen . . .
images_no_of_dividers No. of Dividers No. of Dividers . . . Teilstriche . . .
brackets brackets brackets . . . Klammern . . .
subscript subscript subscript . . . tiefgestellt . . .
news-tag-1.1-alpha-title +++ This is Olex2 Version 1.1-alpha +++ . . . . +++ Dies ist Olex2 Version 1.1-alpha +++ . . .
news-tag-1.1-alpha This is the alpha version of the current 1.1 release of Olex2. This version will be updated very frequently, and you can expect things to go wrong from time to time. You are welcome to use this version - and if you come across anything that isn't quite right, please let us know so that we can fix it. . . . . . . . .
news-tag-1.1-beta-title +++ This is Olex2 Version 1.1-beta +++ . . . . +++ Dies ist Olex2 Version 1.1-beta +++ . . .
news-tag-1.1-beta This beta version of the current 1.1 release of Olex2 has seen some testing in alpha, but isn't quite ready to be updated to the full release version yet. This version should not have any serious bugs - so, if one of them comes crawling your way, please let us know as soon as you can that things aren't quite right. . . . . . . . .
news-tag-1.1-title Welcome to Olex2 Version 1.1 . . . . . . . .
news-tag-1.1 This is our current release version of Olex2. This release version will be updated only after we have gone through subsential testing using the alpha and beta versions of our software. If you would like more frequent updates, please also install these other testing versions. Multiple installations of Olex2 do not interfere with each other. . . . . . . . .
graduated Graduated Background . . . . Verlaufshintergrund . . .
htmlpanelswap-target Swap side of HTML panel . . . . Seitenwechsel . . .
swapbg Colour/White BG . . . . Tapetenwechsel . . .
French French . . . . French . . .
htmlpanelswap Swap HTML Panel . . . . Seitenwechsel . . .
swapbg-target Swap the background from the user defined colour to white . . . . Hintergrundwechsel Benutzerdefinierte Farbe nach Weiss und umgekehrt . . .
graduated-target Switch graduated background on/off . . . . Verlaufshintergrund An/Aus . . .
cf-help There are various settings available that will influence the Charge Flipping Solution. && ~AMPT~ Charge flipping can be done on F, E or quasiE. ~MAPT~Maximum Attempts to find a Phase Transition ~MACM~Maximum Attemtps to get sharp Correlation Map ~MASI~Maximum Number of Solving Iterations && . . . . . . . .
news-1.1-image-headline Fully interactive maps are now available from Tools>Maps. . . . . . . . .
change_element-target Change atom types to . . . . . . . .
Rotate-help Using this tool, you can control the rotation of the molecule on the screen in a somewhat more fine-grained and repeatable compared to what can be achieved with the mouse. && ~Rotate around the axis x, y and z~Enter the degrees of rotation into the spin boxes, then press the buttons to rotate either in the negative or positive direction. ~Even finer control~Using the command line, rotation about fractions of degrees are also possible: XX rota 2 -10.2 XXThis will rotate the structure around the y axis by -10.2 degrees. && . . . . . . . .
anaglyph Anaglyph . . . . . . . .
Normal View Normal View . . . . . . . .
Stereo Stereo . . . . . . . .
Y:-target Rotate around Y . . . . . . . .
:Y-target Rotate around Y . . . . . . . .
X:-target Rotate around X . . . . . . . .
:X-target Rotate around X . . . . . . . .
:Z-target Rotate around Z . . . . . . . .
Z:-target Rotate around Z . . . . . . . .
view-rotate-target View along crystal axis a . . . . . . . .
Res Res . . . . . . . .
Delete Mask Display Delete Mask Display . . . . . . . .
Solvent rad. Solvent rad. . . . . . . . .
Extended Extended . . . . . . . .
Distance Distance . . . . . . . .
Calculate Mask Calculate Mask . . . . . . . .
Precise Precise . . . . . . . .
Res. factor Res. factor . . . . . . . .
Shrink trunc. rad. Shrink trunc. rad. . . . . . . . .
masks-help This is a solvent masking procedure similar to the SQUEEZE procedure implemented in the PLATON software, and described by P. van der Sluis and A. L. Spek, Acta Cryst. (1990). A46, 194-201. && @Displaying the mask@ ~mask~ Displays the solvent accessible area. ~f_mask~ Displays the Fourier transform of the solvent contribution to the structure factors. ~f_model~ Displays the Fourier transform of the sum of contributions to the structure factors of the solvent region and the ordered part of the structure. @Parameters@ ~Resolution factor~ The grid step is chosen to be approximately equal to the high resolution limit multiplied by the resolution factor. ~Solvent radius~ All grid points that are a distance greater than the sum of the van der Waals radius of an atom and the solvent radius are initially set to be inside the solvent area. ~Shrink truncation radius~ All grid points outside the solvent area are then tested to see if they fall within a distance defined by the shrink truncation radius of the solvent area. If this is case, they are added to the solvent area. ~Use set completion~ If low angle reflections are missing (even one is sometimes enough), the electron count can be underestimated. If this option is selected, missing reflections are filled in and allowed to 'float' throughout the Fourier transform iterations, resulting in more accurate estimates of the true electron count.TT mapping_and_masks,masks-help TT && . . . . . . . .
xgrid-help &&@Available Display Modes@ ~contour, plane~ This is an interactive slice of the map in the plane of the screen. The molecule can be rotated and also zoomed through this plane. This is done by holding down the SHIFT key while dragging the left mouse key on the area of the map or using the depth slider. The visible area of the map can be adjusted with the size slider, or by holding down the CTRL key whilst dragging the right mouse. Finally, the levels can be adjusted with the SHIFT key and right mouse. In contour mode, the number of contours can be altered with the contours slider. Positive electron density is displayed as solid lines, whilst negative electron density (holes) are displayed as dashed lines. A contour map will be included in any postscript drawing created whilst the map is displayed.~surface, wire, point~ These are all three dimensional displays of the electron density. However, the 3D display will only work if there is enough electron density to display, otherwise the 2D display will the shown. It is a good idea to start adjusting the levels in the points view, and only then to select wire or surface for a graphically more demanding display. Negative values of electron density (holes) will be displayed in a reddish colour. The extended mode will extend the grid to an array of 27 (3 x 3 x 3) unit cells~Select Volume~ A box with moveable sides will appear. Left-click on the coloured areas and then move the sides while pressing the SHIFT key. The map will be calculated only inside the defined box. You can delete the box by right-clicking on it and select 'Hide'TT mapping_and_masks,xgrid-help TT&& . . . . . . . .
refine-masks-help Include in the refinement a solvent contribution to the structure factors as a discrete Fourier transform of the electron density in the solvent area. When used with smtbx-refine, the solvent contribution is added internally to that calculated from the ordered part, whilst with SHELXL the solvent contribution is subtracted from the observed data before passing a modified hkl file to the external refinement program. . . . . . . . .
Uiso-Select-Slider-help This tool allows the selection of atoms according to their Ueq values. && ~Slide to the RIGHT~ This will select atoms where the Ueq value is LARGER than the value indicated by the slider. XX sel atoms where xatom.uiso > 0.06&&xatom.type!='Q' XX ~Slide to the LEFT~ This will select atoms where the Ueq value is SMALLER than the value indicated by the slider. XX sel atoms where xatom.uiso < 0.06&&xatom.type!='Q' XX && . . . . . . . .
refinement-masks-help In some structures, solvent disorder can be so severe that modelling this disorder using atomic sites (i.e. partially occupied atoms) is neither possible nor sensible. In these cases, it is better to not not even attempt to model the 'affected area' - but to simply leave the measured electron density in place. This technique requires the calculation of the area that should be 'taken out of the refinement' - and defining THAT depends on the current structure.&&~Defining the volume to be masked~ ~Use solvent mask~ Include in the refinement a solvent contribution to the structure factors as the discrete Fourier transform of the electron density in the solvent area. The solvent mask can be calculated and displayed under Tools > Maps > Masks. When used with smtbx-refine, the solvent contribution is added internally to that calculated from the ordered part, whilst with SHELXL the solvent contribution is subtracted from the observed data before passing a modified hkl file to the external refinement program.~Recompute mask before refinement~ When ticked, the solvent mask will be recomputed before the start of the refinement. This can lead to an improved solvent mask, particularly if the ordered part of the structure was poorly converged before the initial mask search.&& . . . . . . . .
About-help Olex2 v1.1.5 © OlexSys Ltd. 2004 – 2011
Oleg V. Dolomanov, Richard Gildea and Horst Puschmann . . . . . . . .
Complete Fragments Complete Fragments . . . . . . . .
hardware Hardware . . . . . . . .
stereo-hardware-target Stereo is achieved by a special graphics card and monitor . . . . . . . .
stereo-colour-target Simple stereo view. Coloured glasses are required . . . . . . . .
stereo-normal-target Standard view . . . . . . . .
stereo-anaglyph-target More sophisticated stereo view. Coloured glasses are required . . . . . . . .
cif-info-help Olex2 provides a number of tools to make it simple to get a full and correct CIF file ready for publication. && ~Edit Cif Info~ This brings up a text editor which displays the current CIF data items that have been found by Olex2 or entered manually by the user. In this window, items can be modified or removed, or new CIF data items added, and Olex2 will remember these changes independently of the CIF file output by the refinement program. ~Merge Cif~ This merges the CIF data items displayed by Edit Cif Info with the CIF file output by the refinement program. ~Validate Cif~ This validates the current CIF file against the core CIF dictionary, cif_core.dic, printing any errors or warnings that are found to the console. XX ValidateCif XX ~Report~ This creates a new CIF file if necessary (including if the existing one is not up to date with the current model), and merges any CIF data items that are provided by the user, before creating a html structure report. XX Report XX && . . . . . . . .
Restraint Restraint . . . . . . 限制 .
History Tree History Tree . . . . Verlaufsbaum . 编辑历史 .
Bijvoet-differences-NPP-help && ~Bijvoet differences probability plot~ For further information see:
Hooft, R.W.W., Straver, L.H., Spek, A.L. (2008). J. Appl. Cryst., 41, 96-103.
Hooft, R.W.W., Straver, L.H., Spek, A.L. (2010). J. Appl. Cryst., 43, 665-668.
www.absolutestructure.com && . . . . . . . .
Bijvoet-differences-scatter-plot-help && ~Bijvoet differences scatter plot~ For further information see:
Hooft, R.W.W., Straver, L.H., Spek, A.L. (2008). J. Appl. Cryst., 41, 96-103.
Hooft, R.W.W., Straver, L.H., Spek, A.L. (2010). J. Appl. Cryst., 43, 665-668.
www.absolutestructure.com && . . . . . . . .
submit-info-help && ~Get Checkcif Report~ This will send your cif file to the IUCr server specified in the settings for checking. The result will be displayed in your web browser and saved to your structure directory. XX spy.getCheckCifReport()XX ~Request CCDC Number~ This utility will upload your cif and fcf file to the Cambridge Structural Database. Once your files are processed in Cambridge, you will receive an e-mail with the CCDC Number, which is required for publication of crystal structures in many journals. XX spy.ccdc_submit()XX && . . . . . . . .
toolbar-hydrogen_1-help Normally, you would generate the hydrogen atom positions automatically using the HADD command. However, sometimes you might want to specify the hydrogen types manually. && ~Mode HFIX~ Body text XX hfix
Select three atoms, starting from one of the 'outer' atoms, then the middle one, then the other outer one.
In the example below, the angle between the three atoms will be restrained to 108 degrees and the distance between the central atom and the two outer atoms will be 0.85A. The order in which the numbers are provided does not matter. XX tria 109 0.85 XX && . . . . . . . .
Documentation Documentation . . . . . . . .
QuickDemo QuickDemo . . . . . . . .
PDF PDF . . . . . . . .
Analyse π-π Interactions None . . . . . . . .
ccdc-submission-options-help There are three 'types' of submission to the CCDC: && ~Private Communication~ The structure is not intended for publication, but I wish to make it available to other scientists through the CSD. I am therefore authorising the CCDC to include this data directly into the CSD. ~Ready to Publish~ This work will be published in the journal as indicated in the cif file. Please make sure that Journal name, volume, page and year are all filled in (Report > Report Settings > Publication) ~Unsure~ If any structure is not published within three years and no instructions have otherwise been received, the CCDC will attempt to contact you and the corresponding author by e-mail. If no response is obtained, the CCDC will retain the data indefinitely pending future publication. && . . . . . . . .
fit-group-help This tool operates on a selection of atoms, which can consist of any number of atoms. && ~Move One Atom~ Select one atom, then select whether you want to fit or split the atom. If you want to fit the atom, you can now move that atom with the left mouse to any position you like by pressing the SHIFT key; when you are finished, press the ESC button. If you want to split the atom, you will now see TWO atoms, both of which you can move with the left mouse while holding the SHIFT key pressed. The occupancies of the two atoms are linked, and the atoms will now belong to different parts. ~Move Two Atoms~ Select two atoms, then select whether you want to fit or split the group. Split will generate a duplicate group, fit will not.
While pressing the SHIFT key, you can move the selection as a group. While pressing the CTRL key, you can rotate the group around the midpoint between the two atoms. ~Move Three or more Atoms~ Select three or more atoms, then select whether you want to fit or split the group. Split will generate a duplicate group, fit will not.
While pressing the SHIFT key, you can move the entire group. You can now activate any bond around which you wish to rotate the group by right-clicking on it. While pressing the CTRL key, you can rotate the group around this activated bond.