Dear Sabine, if you are using bash (or probably any other POSIX compliant shell more sophisticated than sh), rename your PDB-file to myfile001.pdb and you should be able to use something like this:
#!/bin/bash
for i in $(seq 100); do
pdbset xyzin myfile$(printf "%03d" $i).pdb \
xyzout myfile$(printf "%03d" $((i + 1)) ) << eof
shift 10 0 0
rotate matrix 0.9848 -0.1736 0 0.1736 0.9848 0 0 0 1
end
eof
Where the entries of the rotation matrix are explained e.g. on wikipedia (this
example rotates about the z-axis and shifts along x).
You could also use moleman2 instead.
Cheers, Tim
On Fri, Feb 18, 2011 at 03:54:58PM +0100, Sabine Schneider wrote:
> Hello,
>
> I want to apply to a small structure a rotation and translation (i.e
> 10A translation and 10dg rotation), write out the coordinates and
> apply the same rotation/translation to the new coordinates and
> repeat this lets say 100 times.
>
> I guess the program of choice would be pdbset but I am not sure how
> to script it to do the repetition?
>
> Thanks a lot for your help!
>
> Sabine
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Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
phone: +49 (0)551 39 22149
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