[Chimera-users] crystallographic symmops and lattice translationsin Chimera

Boaz Shaanan bshaanan at bgu.ac.il
Sun Dec 16 02:54:17 PST 2007

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.



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 at cgl.ucsf.edu>
Date: Sunday, December 16, 2007 2:29
Subject: Re: [Chimera-users] crystallographic symmops and lattice translationsin Chimera
To: Boaz Shaanan <bshaanan at bgu.ac.il>
Cc: chimera-users at 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
Phone: 972-8-647-2220 ; Fax: 646-1710
Skype: boaz.shaanan‎
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