[MMTK] applyto with c_terminus=1 protein structure

ra.biehl ra.biehl at fz-juelich.de
Thu Mar 24 15:13:28 UTC 2011


  Hi

I have a sequence of proteins structures with the same content but
different atom positions from an MD run as a pdb file with model
sections 1 to 200

I can load the individual configurations with

 >conf1 = PDBConfiguration('xx001')
 >chain=conf1.peptide_chains[0].createPeptideChain(c_terminus=1)
 >universe.addObject(chain)
and i can work with the universe

to change only the coordinates to a second configuration
 >conf2 = PDBConfiguration('xx002')
 >conf2.applyTo(universe[0])
i get the message
 >Warning: 3231 atom(s) were not assigned (new) positions.

using
 >chain=conf1.createAll()
IOError: Atom O1 of PDB residue LYS not found in residue Lys of object
.Lys415
because i cannot tell create all about the c_terminus
The first way also fails without c_terminus=1 in a modified protein
structure (del O2, rename O1 in O in Lys415)

My goal is just to analyze a sequence of configurations with the same
structure but different positions.
It could be done by reading the pdb files as trajectory and walking trough,
but i didnt find a way.

Hope someone can help

Best
Ralf






--

Dr. Ralf Biehl
Jülich Centre for Neutron Science (JCNS-1)&
Institute for Complex Systems (ICS-1)
Forschungszentrum Jülich
52425 Jülich
Germany

Tel.:   +49-(0)2461-61-4685
Fax:    +49-(0)2461-61-2610
Email:  ra.biehl at fz-juelich.de
Web:    http://www.fz-juelich.de/iff/d_ins


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