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This section contains some typical input data sequences for crystallographic calculations. These trace the basic steps from the data reduction of the raw diffraction intensities to the preparation of the publication material. The Xtal system divides these different steps of an analysis into separate calculation models. Users must learn which module does what and how these can be chained together in the best way to suit the study. The archive bdf's provide the main communication link between calculations with the auxilliary files supplying a specific data link between some calculations. Usually several crystallographic calculations are performed together. The number of calculations in each run will vary according to the nature of the analysis and the expertise of the user. In fact, the length of the run is usually dictated by how often the user wishes to check how the calculations are proceeding. Between these runs the archive and auxilliary files retain the history and the accumulated knowledge of the calculation sequence. Other example inputs are given with the program descriptions. More detailed examples are provided as the supplied test input files p6122.dat , saly.dat , diam.dat , ags4.dat and lac1.dat . Novice Xtal users are advised to print these files as an additional reference. The first step in any analysis is to enter the
primary crystallographic information such as cell, symmetry
and chemical formula. In
Xtal this is usually done with the
program
compid exampl title study of the compound C23 H28 O6 P212121 Z=4 STARTX cell 17.076 16.604 7.425 90. 90. 90. cellsd .004 .002 .007 sgname P 2ac 2ab : H-M notation P212121 celcon C 92 celcon O 24 celcon H 112 Note that it is possible start an analysis with CIF input as well (using CIFIO) because this automatically invokes the STARTX routine in the process. The next step, after creating the initial archive
file, is to input the reflection data. This may be done in
a number of different ways using
If the reflection data are raw intensities or counts from a diffractometer then there needs to a calculation that reads this data and scales it for conversion to structure factors. DIFDAT is usually used to process a diffractometer file. Here is a control sequence for processing a standard
Siemens ascii file labelled
compid.sie. DIFDAT reads this file and
stores the scaled intensities on the archive file. ADDREF
reads the archive file and reduces the intensities into
structure factors (note that ADDREF stores both |Fmeas| and
|Fmeas| squared on the archive file). The other data such
as diffractometer angles are not entered (ie. absorption
corrections will not be applied). If they were on would
place
DIFDAT sie baln 3 genscl ADDREF reduce itof rlp4 12.2 bdfin hkl irel sigi
If one is entering reflection data that has already been scaled it may be entered as part of the .dat file as follows.
ADDREF reduce itof rlp4 12.2 hklin hkl rcod irel sigi hkl 0 0 2 1 21023 644 hkl 0 0 4 1 40 5.97 hkl 0 0 6 1 252 11.4 hkl 0 0 8 1 33.4 4.9 .................................reflection data omitted for brevity hkl 19 11 0 2 .214+00 .333+01
Other initial reflection processing calculations are
provided by programs such as
SORTRF order hlk aver 1
Look carefully at the examples given in the program descriptions. The next step is to determine the crystal structure.
This can be done with a variety of ways. The most automatic
approach is to use the new iterative solution program
CRISP Another direct methods approach which does not
involve the automatic iterative program CRISP, uses the
programs
GENTAN FOURR emap PEKPIK PIG For some centrosymmetric structures it may be more effective to run SIMPEL FOURR emap PEKPIK PIG Or in difficult cases where a fragment of the structure is known one should try the sequence GENEV GENSIN FOURR epat PATSEE Alternatively the user can apply the heavy atom
method wth a combination of the programs
In these seqquences the program GENEV calculates the
E values needed for direct methods. GENSIN generates
triplets and quartets and outputs them to the auxiliary
file
The FOURR program inputs the phases estimated by
GENTAN to produce an E map. This map is output to the file
In the event that solution programs such as CRISP, GENTAN, SIMPEL or PATSEE do provide a clear solution of the initial structure, it may be necessary to adjust the standard options used in these calculations. Here is some general advice on the optimal use of these routines. Note that in the above example input only a few command lines are needed. This is because the default controls are appropriate for most analyses. For some analyses additional control signals may be required. Here are some tips for the application of the direct methods programs.
For structures not solved with the default options, try the following alternatives separately. Note that the judicious saving of the bdf's permits you to start calculations at the program in which the option needs to be changed. Do not always start with STARTX, or even GENEV!
When assessing a direct methods run for success or failure, do not rely wholly on the GENTAN or SIMPEL figure of merit estimates. For some structure types these will be unreliable. It is good practice to calculate the E maps for the top four (or even eight) phase sets and then look closely at the PEKPIK results. One or two dominant peaks usually signals an incorrect phase set (except if there one or two heavy atoms in the structure!). The best E maps contain a large number of medium height peaks and this may be used as a quite sensitive criterion for identifying the more correct phase sets. There are many other combinations of options available in GENSIN and GENTAN. If the above alternatives fail you should look critically at the reflection data, both in terms of its precision and high angle limit, and at the possibility of incorrect space group symmetry. In some cases structures are solved automatically by recollecting the data with better precision and/or higher angle data. In cases where there are very high B-values it may be necessary to collect low-temperature data. It cannot be emphasised enough that these methods are very dependent on good E-values. GENEV works well with good data, but if the Wilson plot shows anomalies at high angles it is better to exclude this data from the structure solution (by setting Smax in GENEV). Always check the Wilson plots carefully if the default run fails. Once a structure is determined the coordinate and displacement parameters need to be refined. A variety of programs are needed for a refinement sequence. Often the initial atomic coordinates are loaded onto the archive file by PEKPIK and PIG. In other instances all, or same, of the coordinates will need to be loaded with ADDATM. In this simple example ADDATM is used to load atom
data and
ADDATM scale 1.02033 1 atom C1 .48236 -.11502 .93088 .0332 1.0 .00023 .00024 .00053 uij C1 .00244 .00391 .01162 -.00008 .00009 -.00021 atom O1 .47364 -.18767 .83988 .0385 1.0 .00017 .00015 .00039 uij O1 .00378 .00323 .01594 -.00027 -.00053 .00071 .......................................atom data omitted for brevity atom H6 .75500 -.10800 .93600 .0570 1.0 .00000 .00000 .0000 atom H7 .64700 -.14500 1.20600 .0680 1.0 .00000 .00000 .0000 atom H81 .81360 -.11540 1.23320 .0740 1.0 .00000 .00000 .0000 atom H82 .79070 -.20340 1.18740 .0740 1.0 .00000 .00000 .0000 atom H83 .78040 -.17080 1.37730 .0740 1.0 .00000 .00000 .0000 CRYLSQ cy 2 ad fm fu 0.7 : CRILSQ could be used instead noref H RSCAN PIG BONDLA
This sequence emphasises the modularity of Xtal calculations. There are many other combinations involving many programs. For example, when atoms are still missing from the model (or one is searching for the H atom sites) the following combination is very useful.
CRYLSQ cy 2 noref H FOURR fdif PEKPIK PIG input peaks prad 1.
Here the program PIG is used to decide which peak sites are to become atom sites (and are labelled) and which should be rejected Periodically during an analysis the model and refined
structure factors need be checked. The model can, of
course, be monitored with PIG, but many other checking
tools are provided in the
Xtal system. These include
Here is one sort of run which also inserts H atom sites from the non H atom geometry.
BONDLA cont dihe atrad H 1. .5 FOURR fdif r2 0 PEKPIK punch BONDAT calcat tetchn 0.95 O5 C1 C2 H1 H11 calcat teterm 0.95 C1 O1 C11 H111 H112 H113 calcat tetchn 0.95 C1 C2 C3 H21 H22 calcat tetchn 0.95 O2 C21 C22 H211 H212 calcat trigon 0.95 C22 C23 C24 H23 calcat trigon 0.95 C23 C24 C25 H24 calcat trigon 0.95 C24 C25 C26 H25 calcat tetchn 0.95 C3 C4 C5 H41 H42 calcat tetchn 0.95 C4 C5 O5 H51 H52 calcat teterm 0.95 C6 C7 C8 H81 H82 H83
When the structure is ready for publication various molecular plots, and tables need to be prepared. Here are some of the calculations that can be used for this purpose.
BONDLA LSQPL PLANE DEFINE C22 C23 C24 C25 C26 C27 nondef O2 C21 PLANE DEFINE C32 C33 C34 C35 C36 C37 nondef O3 C31 PIG ORTEP mole acta PREVUE PLOTX postl pre LISTFC nofl wid 120 lin 64 ATABLE isou CIFIO cifo
The examples shown above are a very small sample of
the combinations possible with
Xtal programs. A novice user should
experiment with input sequences using known data so that
there will be a proper understanding of the various
functions. And always remember that the archive bdfs
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