crystallographic symmops and lattice translations in Chimera
Hi, Since the question was raised before, I think I know the answer to my first question about lattice translations but let me verify: 1) Chimera can apply crystallographic symmetry operations to the model as they're listed in the pdb file but it won't apply lattice translations, or in other words, won't display molecules in neighbouring unit cells. Am I correct ? maybe you can surprize me me on this and prove me wrong ? 2) Is it possible to draw the unit cell boundaries after reading in the pdb or should I read in a dummy pdb with coordinates of the unit cell vertices ? Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan
Hi Boaz, Chimera can apply lattice translations in a variety of ways, though there isn't currently a simple flexible command for this. The Multiscale tool (menu Tools / Higher-Order Structure) can make a 3 by 3 by 3 array of unit cells, and you can drag to select and delete unwanted monomers. The Unit Cell tool (same menu) can translate the unit cell origin (values 0-1) and reposition all asym units to have their centers in the cell. That only allows translation by a fraction of a unit cell. The Crystal Coordinates script on the experimental features web page can write out PDB files for a block of unit cells. That has to be downloaded separately: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html Another trick is you could open two copies of your PDB translate one by one unit cell length along x with a command line "move x 123.5" then apply the Unit Cell tool to both copies. You'd have to get the unit cell size in x by looking at the CRYST1 record in the PDB file. The Unit Cell tool has a button "Outline unit cell" that displays an outline box for the unit cell of a chosen PDB model. Tom
Hi Tom, Thanks so much ! You did surprize me indeed with Chimera capabilities that I wasn't aware of. I'll try your suggestions very soon. Cheers, Boaz P.S. We have a Nature Chemical Biology paper coming up soon with some Chimera pictures in it (and in the supplementary online material). I'll send the pdf's once it's online. ----- Original Message ----- From: Tom Goddard <goddard@cgl.ucsf.edu> Date: Sunday, December 16, 2007 2:29 Subject: Re: [Chimera-users] crystallographic symmops and lattice translationsin Chimera To: Boaz Shaanan <bshaanan@bgu.ac.il> Cc: chimera-users@cgl.ucsf.edu
Hi Boaz,
Chimera can apply lattice translations in a variety of ways, though there isn't currently a simple flexible command for this. The Multiscale tool (menu Tools / Higher-Order Structure) can make a 3 by 3 by 3 array of unit cells, and you can drag to select and delete unwanted monomers. The Unit Cell tool (same menu) can translate the unit cell origin (values 0-1) and reposition all asym units to have their centers in the cell. That only allows translation by a fraction of a unit cell. The Crystal Coordinates script on the experimental features web page can write out PDB files for a block of unit cells. That has to be downloaded separately:
http://www.cgl.ucsf.edu/chimera/experimental/experimental.html Another trick is you could open two copies of your PDB translate one by one unit cell length along x with a command line "move x 123.5" then apply the Unit Cell tool to both copies. You'd have to get the unit cell size in x by looking at the CRYST1 record in the PDB file.
The Unit Cell tool has a button "Outline unit cell" that displays an outline box for the unit cell of a chosen PDB model.
Tom
Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan
participants (2)
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Boaz Shaanan -
Tom Goddard