Re: [Jmol-users] symmetry operations on pdb file

[Bob H. <ha...@st...>]

Why not just load the model as a full unit cell:

load xxxx.pdb {1 1 1}

No?


Angel Herraez wrote:

>Hi
>I'm trying to apply symmetry operations to a pdb file, to generate 
>shifted copies of the molecule. 
>This is the crystal info in the pdb file:
>CRYST1   39.970   26.950  677.900  89.24  94.59 105.58 P 1           
>2          
>ORIGX1      1.000000  0.000000  0.000000        0.00000               
>          
>ORIGX2      0.000000  1.000000  0.000000        0.00000               
>          
>ORIGX3      0.000000  0.000000  1.000000        0.00000               
>          
>SCALE1      0.025019  0.006976  0.002068        0.00000               
>          
>SCALE2      0.000000  0.038521  0.000330        0.00000               
>          
>SCALE3      0.000000  0.000000  0.001480        0.00000               
>          
>
>The same file says that to replicate the molecule, these translations 
>must be used: -1, 0,-1;   -2, 0,-2;  etc.
>
>So I tried loading the model several times (a great recent hint by 
>Bob) using "load files" and then use "translateSelected" on each 
>model.
>However, I am not getting the positions I expected. 
>I think I may be missing something; is there a chance that I am doing 
>the translation along the coordinate axes instead of along the 
>symmetry axes? (unit cell edges). Not sure, as I have no experience 
>in crystallography.
>
>The news sectio says that from 11.0 arbitrary space groups and unit 
>cells may be defined for any model from any file format. I think this 
>is what I need, but don't know how to do it. How to make Jmol use the 
>crystal info in the pdb?
>
>Any help will be welcome.
>
>
>
>
>
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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get. 

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900