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