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Hi Mike,<br>
<br>
The space groups recognized by the Unit Cell tool are defined in the
Chimera distribution in file<br>
<br>
chimera/share/Crystal/space_groups.py<br>
<br>
(On the Mac this is
Chimera.app/Contents/Resources/share/Crystal/space_groups.py.) That is
Python code and you can look at it in any text editor. Look at the
table at the end of the file. A few years ago I made this file and I
tried to include every space group listed in a Protein Databank entry
though I may not have succeeded. Are the non-centrosymmetric groups
used by the PDB?<br>
<br>
A fallback is to just specify exactly the symmetries that build the
unit cell from the asymmetric unit using PDB REMARK 290 SMTRY records.
Can be inconvenient, but if those symmetries are already present in a
different PDB entry you can copy and paste them.<br>
<br>
More detail on Unit Cell is in the User's Guide.<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.html">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.html</a><br>
<br>
If you have suggestions for how to improve it, tell me. I have to warn
you that we've really focused on electron microscopy density map
analysis in Chimera and our x-ray map capabilities are rough.<br>
<br>
Tom<br>
<br>
<br>
-------- Original Message --------<br>
Subject: [Chimera-users] Centro-symmetric space groups<br>
From: Michael Day <br>
To: <a class="moz-txt-link-abbreviated" href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a><br>
Date: 8/28/09 3:25 PM<br>
<blockquote cite="mid:10F90B7A-E56C-41F9-B362-7643E30127B6@caltech.edu"
type="cite">How do you get Chimera to recognize centrosymmetric space
groups.
<div><br>
</div>
<div>If I include the space group on the CRYST1 card of the PDB file
all is well for non-centrosymmetric groups but when a center of
symmetry enters the picture all bets are off.</div>
<div><br>
</div>
<div>I'm using Tool->Higher-Order Structure->Unit cell</div>
<div><br>
</div>
<div>For example adding the space group in column 56 of the PDB</div>
<div>P1 as P 1 - all's good</div>
<div>P-1 as P -1 - complete nonsense although it recognizes there are
two symmetry elements</div>
<div>P2 as P 1 2 1 - all's good</div>
<div>P21 as P 1 21 1 - all's good</div>
<div>P212121 as P 21 21 21 - no problem</div>
<div>But;</div>
<div>P21/c as P 1 21/c 1 - no recognized symmetry elements and no
unit cell expansion.</div>
<div><br>
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<div>Cheers,</div>
<div>Mike</div>
<div><br>
</div>
<div><<<
------------------------------------------------------------------------>>></div>
<div>Dr. Michael W. Day</div>
<div>Director - X-ray Crystallography Lab & Molecular Observatory</div>
<div>California Institute of Technology</div>
<div>Mail Code 139-74</div>
<div>Pasadena, CA 91125</div>
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