[Chimera-users] Fwd: CCL: Coordinate system rotation

Elaine Meng meng at cgl.ucsf.edu
Thu Jun 19 15:28:03 PDT 2014


On Jun 19, 2014, at 8:33 AM, "Radoslaw Kaminski rkaminski.rk,+,gmail.com" <owner-chemistry at ccl.net> wrote:

> Sent to CCL by: "Radoslaw  Kaminski" [rkaminski.rk]=[gmail.com]
> Dear All,
> 
> A trivial question. I have a XYZ file with a molecule in some coordinate 
> system. I would like to have a Z axis be in a certain direction along A...B 
> atoms. Is there any program that can easily change my coordinate system by 
> choosing some 3 atoms? I can of course do all transformations by hand (for 
> example in Excel) but its tedious. I know that ADF is capable of transforming 
> the coordinates to some specified coordination system (Prof. Baerends' CCL post 
> from several years ago), but is there any other program that can just make such 
> transformations quickly?
> 
> Thanks in advance,
> Radek


From: Elaine Meng <meng at cgl.ucsf.edu>
Subject: Re: CCL: Coordinate system rotation
Date: June 19, 2014 9:57:00 AM PDT

Hi Radek,
With Chimera you could align 2 atoms front->back and then save a PDB file with the transformed coordinates.  Not sure if that is exactly what you needed, or whether it is quick enough, but you could automate looping through multiple files with a little bit of Python.

(1) open XYZ file (e.g. menu File…Open, choose file.xyz, or command "open file.xyz")
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/xyz.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/open.html>

That will automatically assign unique atom names by element and order in file, for example the first C will be C1, the first N will be N1.

(2) use "align" command to put atoms A,B  in center of view along the line of sight (laboratory Z axis) with A in front and B in back (e.g.: align @c1 at o1)
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/align.html>

(3) save PDB with transformed coordinates (e.g. menu File…Save PDB, un-check "use untransformed coordinates" or command something like "write #0 file.pdb")
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html>

(4) close structure (e.g. command "close #0" or "close all") … if multiple structures to process, loop back to step 1.  See here for writing looping scripts for Chimera:
<http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco





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