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
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