Dear Chris,
The script might work technically, but applying the same
transformation matrix 100 times to the output of the previous
iteration is a recipe for disaster. PDB files only store
coordinates to 3 decimal places and your rounding errors will
build up horribly.
Far better to work out the transformation matrix/vector
required for each iteration and apply that set to the original
coordinates.
Regards,
Robert
--
Dr. Robert Esnouf,
University Research Lecturer
and Head of Research Computing,
Wellcome Trust Centre for Human Genetics,
Roosevelt Drive, Oxford OX3 7BN, UK
Emails: rob...@strubi.ox.ac.uk Tel: (+44) - 1865 - 287783
and rob...@esnouf.com Fax: (+44) - 1865 - 287547
---- Original message ----
>Date: Wed, 27 Jun 2012 09:03:13 +0000
>From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> (on behalf
of "Froehlich, Chris" <chris.froehl...@mdc-berlin.de>)
>Subject: [ccp4bb] apply a spatial transformation on a pdb
file n times
>To: CCP4BB@JISCMAIL.AC.UK
>
> Dear colleagues,
>
>
>
> I want to apply a given
> x-y-z-rotation/transformation matrix on a pdb file,
> save the new pdb file and apply the same matrix
> again on the new pdb file and repeat this e.g. 100
> times, thereby saving all pdb files (i.e. 01.pdb,
> 02.pdb, 03.pdb etc.).
>
>
>
> With pdbset this is very easy, but I'm wondering if
> there is any script to do so because I don't want to
> manually change file names all the time...
>
> I am not very familiar with scripting, but I found
> something in the internet.
>
> Can anybody help please with this i.e. is this a
> reasonable script to do so?
>
>
>
> # repeat a spatial transformation on a pdb file n
> times.
>
> #!/bin/csh -f
>
> start n=1 until n=x.
>
> pdbset xyzin mypdbfile($n).pdb xyzout
> mypdbfile($n+1).pdb <<eof-1
>
> transform -
>
> 0.87831 0.47808 0 0 0 -1. -0.47808
> 0.87831 0 0.0 -2.713 0.0
>
> eof-1
>
>
>
>
>
> Thanks a lot,
>
> Chris
>
>
>
>
>
>
>
>
>
> DIPL.-ING. CHRIS FRÃ*HLICH
>
> Crystallography Dept. | Daumke group
> Max-Delbrück-Centre for Molecular Medicine (MDC)
> Robert-Rössle-Str. 10
> 13125 Berlin-Buch
> Lab: +49(0)30-9406-3263
> Office: +49(0)30-9406-3275
> Fax: +49(0)30-9406-3814
>
>
>
> www.mdc-berlin.de/daumke
>
>
