[MMTK] problem with findTransformation

[Jaroslaw Kalinowski]

   Hi,

I tried to align two structures but I could not obtain proper fit. I did:

import MMTK
import MMTK.PDB
import MMTK.Proteins

pdb_u = MMTK.PDB.PDBConfiguration('U.pdb').peptide_chains[0]
pdb_b = MMTK.PDB.PDBConfiguration('B.pdb').peptide_chains[0]
p = MMTK.Proteins.PeptideChain(pdb_b, model='no_hydrogens', c_terminus=0)
u = MMTK.InfiniteUniverse()
u.addObject(p)
cb = MMTK.copy(u.configuration())
pdb_u.applyTo(p)
transformation, rms = p.findTransformation(cb)
p.applyTransformation(transformation)
MMTK.PDB.PDBOutputFile('UonB.pdb').write(p)
print 'RMS = %.3f [nm]' % rms


U.pdb contains 42 lines from 132L.pdb, form
ATOM      1  N   LYS     1      -9.649  18.097  49.778  1.00 20.73   1  132L  90
to
ATOM     42  NH2 ARG     5       3.197   5.868  41.064  1.00 20.27      132L 131

B.pdb contains 42 lines from 1MEL.pdb, from
ATOM   1951  N   LYS L   1      23.112  46.321  20.224  1.00 18.55           N
to
ATOM   1992  NH2 ARG L   5      27.529  37.902  37.322  1.00 15.78           N

I have enclosed them as attachments but they shall be probably filtered.

Obtained UonB.pdb file contains a structure that is centered on 
the structure from B.pdb but only roughly oriented along it.
I tried structural alignment using vmd and it gave a lot better fit. 
For example: the distance between ARG5:CB obtained using MMTK is 2.7A and 
using vmd it is only 0.18A. MMTK's RMS = 0.044 [nm].

Is there something wrong with my code?

Thanks in advance.

   Jaroslaw Kalinowski
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