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: [email protected] Tel: (+44) - 1865 - 287783 and [email protected] Fax: (+44) - 1865 - 287547 ---- Original message ---- >Date: Wed, 27 Jun 2012 09:03:13 +0000 >From: CCP4 bulletin board <[email protected]> (on behalf of "Froehlich, Chris" <[email protected]>) >Subject: [ccp4bb] apply a spatial transformation on a pdb file n times >To: [email protected] > > 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 > >
