Centro-symmetric space groups
How do you get Chimera to recognize centrosymmetric space groups. 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. I'm using Tool->Higher-Order Structure->Unit cell For example adding the space group in column 56 of the PDB P1 as P 1 - all's good P-1 as P -1 - complete nonsense although it recognizes there are two symmetry elements P2 as P 1 2 1 - all's good P21 as P 1 21 1 - all's good P212121 as P 21 21 21 - no problem But; P21/c as P 1 21/c 1 - no recognized symmetry elements and no unit cell expansion. Cheers, Mike <<< ------------------------------------------------------------------------>
Dr. Michael W. Day Director - X-ray Crystallography Lab & Molecular Observatory California Institute of Technology Mail Code 139-74 Pasadena, CA 91125
<>< <>< <>< <>< <>< <>< <>< <>< <>< <>< Beckman Institute, Room 116 Phone: (626) 395-2734 Fax: (626) 449-4159 e-mail: mikeday@caltech.edu <<< ------------------------------------------------------------------------>
Hi Mike, The space groups recognized by the Unit Cell tool are defined in the Chimera distribution in file chimera/share/Crystal/space_groups.py (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? 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. More detail on Unit Cell is in the User's Guide. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.h... 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. Tom -------- Original Message -------- Subject: [Chimera-users] Centro-symmetric space groups From: Michael Day To: chimera-users@cgl.ucsf.edu Date: 8/28/09 3:25 PM
How do you get Chimera to recognize centrosymmetric space groups.
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.
I'm using Tool->Higher-Order Structure->Unit cell
For example adding the space group in column 56 of the PDB P1 as P 1 - all's good P-1 as P -1 - complete nonsense although it recognizes there are two symmetry elements P2 as P 1 2 1 - all's good P21 as P 1 21 1 - all's good P212121 as P 21 21 21 - no problem But; P21/c as P 1 21/c 1 - no recognized symmetry elements and no unit cell expansion.
Cheers, Mike
<<< ------------------------------------------------------------------------>>> Dr. Michael W. Day Director - X-ray Crystallography Lab & Molecular Observatory California Institute of Technology Mail Code 139-74 Pasadena, CA 91125
<>< <>< <>< <>< <>< <>< <>< <>< <>< <><
Hi Mike, If there is a bug I want to fix it. Give me the example PDB and the correct answer, say from some other software -- best if it were another PDB file with the other asymmetric units in the unit cell. If that is difficult and image might suffice. I'm not clear on what you are saying is wrong. Do you mean the placement of the asymmetric units produced by the Unit Cell dialog for space group "P -1" is wrong? That would be pretty odd -- I'd expect many space groups to give wrong results if there was a bug. If that is the issue, you may be getting tripped up by the fact that the asymmetric units are placed according to the symmetries but then moved so that the center of each asymmetric unit being placed lies within the unit cell box having origin at the location given in the dialog. The purpose of this is to get a packed unit cell. Probably should have an option to disable that behavior so you just get exactly the standard symmetry placement. Tom -------- Original Message -------- Subject: Re: [Chimera-users] Centro-symmetric space groups From: Michael Day To: Tom Goddard <goddard@cgl.ucsf.edu> Date: 8/31/09 4:45 PM
Tom,
Thanks for the info! Especially the speedy response! The PDB definitely allows centrosymmetric groups even though they never appear in proteins.
Centrosymmetric space groups still get mangled. Your file appears to have the right symmetry operators. I ran into this on a P-1 structure that is a stack of planar molecules but when I expand the unit cell I get some thing completely different.
I've tried the PDB file with other viewers and I can get the correct representation but I much prefer Chimera to everything else I've tried (there's really no comparison).
It seems one of the the most straightforward options would be to start with CIF files because they have the symmetry operators in them and the coordinates are the actual crystallographic coordinates and therefore wouldn't need to be transformed/deorthogonalized.
It may be a bug with your deorthogonalization routine.
Cheers, Mike
Hi Mike, Oops. The symmetries that invert coordinates don't work in the Unit Cell tool. This is because it sets the transformation matrix (rotation and shift) for the asymmetric unit copies but it can only handle proper rotations. Chimera is generally used for proteins which are handed (not symmetric under inversion) so such space groups generally don't occur for proteins. But of course for small molecules they can. I'll fix this soon, maybe later this week. I'll have to change atom coordinates instead of setting the transform matrix for the asymmetric unit copies. Tom -------- Original Message -------- Subject: Re: [Chimera-users] Centro-symmetric space groups From: Thomas Goddard <goddard@cgl.ucsf.edu> To: Michael Day <mikeday@caltech.edu> Date: 8/31/09 5:25 PM
Hi Mike,
If there is a bug I want to fix it. Give me the example PDB and the correct answer, say from some other software -- best if it were another PDB file with the other asymmetric units in the unit cell. If that is difficult and image might suffice.
I'm not clear on what you are saying is wrong. Do you mean the placement of the asymmetric units produced by the Unit Cell dialog for space group "P -1" is wrong? That would be pretty odd -- I'd expect many space groups to give wrong results if there was a bug. If that is the issue, you may be getting tripped up by the fact that the asymmetric units are placed according to the symmetries but then moved so that the center of each asymmetric unit being placed lies within the unit cell box having origin at the location given in the dialog. The purpose of this is to get a packed unit cell. Probably should have an option to disable that behavior so you just get exactly the standard symmetry placement.
Tom
-------- Original Message -------- Subject: Re: [Chimera-users] Centro-symmetric space groups From: Michael Day To: Tom Goddard <goddard@cgl.ucsf.edu> Date: 8/31/09 4:45 PM
Tom,
Thanks for the info! Especially the speedy response! The PDB definitely allows centrosymmetric groups even though they never appear in proteins.
Centrosymmetric space groups still get mangled. Your file appears to have the right symmetry operators. I ran into this on a P-1 structure that is a stack of planar molecules but when I expand the unit cell I get some thing completely different.
I've tried the PDB file with other viewers and I can get the correct representation but I much prefer Chimera to everything else I've tried (there's really no comparison).
It seems one of the the most straightforward options would be to start with CIF files because they have the symmetry operators in them and the coordinates are the actual crystallographic coordinates and therefore wouldn't need to be transformed/deorthogonalized.
It may be a bug with your deorthogonalization routine.
Cheers, Mike
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Tom Goddard