Solve a small-molecule structure: Difference between revisions

Solve a small-molecule structure (edit)

Revision as of 12:02, 13 November 2012

318 bytes removed , 13 November 2012

→‎use XPREP to find possible spacegroups

Kay

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 === use [[XPREP]] to find possible spacegroups ===
-First, convert the reflection file to HKLF 4 format (intensities!). The HKLF 4 format is what the SHELX programs read. I used [[xds:XDSCONV|XDSCONV]] and the following XDSCONV.INP:
+There is no longer a need to use [[xds:XDSCONV|XDSCONV]] to convert the XDS_ASCII.HKL reflection file to HKLF 4 format (which is what the SHELX programs read) since XPREP can read XDS_ASCII.HKL directly. Just run
-  SPACE_GROUP_NUMBER=   1
+  xprep
- UNIT_CELL_CONSTANTS=    14.433    28.704     8.488  90.000  90.000  90.000
+without a filename, and when the filename prompt appears, enter:
-  INPUT_FILE=XDS_ASCII.HKL
+  XDS_ASCII.HKL
- OUTPUT_FILE=temp.hkl
+(or whatever you have renamed it to) and then hit <Enter> several times until the program suggests a list of spacegroups - this list is going to be important. It may help to observe whether the data are centrosymmetric or not, from the 8th non-blank line below. Fortunately, this time there's only one spacegroup consistent with the data:
-It is important that - to preserve the full information about systematic absences, for use in [[XPREP]] - XDSCONV runs in spacegroup 1. This does not necessarily mean that CORRECT also has to run in spacegroup 1, because XDS_ASCII.HKL has all observations no matter in which spacegroup the CORRECT step runs. As long as the spacegroup used in the CORRECT step is primitive, this works nicely. But if some re-indexing between CORRECT's spacegroup and P1 is necessary (like in I, F, C, R) then it is probably safest to rather just run CORRECT in P1.
-Run "xprep temp.hkl", answer the question concerning the cell axes, and then hit <Enter> several (about 6) times until the program suggests a list of spacegroups - this list is going to be important. It may help to observe whether the data are centrosymmetric or not, from the line: Mean |E*E-1| = 0.939 [expected .968 centrosym and .736 non-centrosym]. Fortunately, this time there's only one spacegroup consistent with the data:
 <pre>
 SPACE GROUP DETERMINATION
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   HKLF 4
   END
+Compared to the P1 setting that CORRECT chose, XPREP has re-indexed the data in this example such that the conventional setting is obtained for this space group.
+If necessary XPREP can read in several XDS_ASCII.HKL files, scale them together and merge them. However it needs to start with one file to get the space group so that it knows how to merge.
 === use [[ccp4dev:Symmetry_determination_with_Pointless|POINTLESS]] to find possible spacegroups ===