Dear Dr. Charles Schwieters:
I want to refine a protein crystal structure with saxs data. This crystal
structure contain two domains connected by two flexible loops. I met two
problems before the refinement.
First, the crystal structure missed some residues in the loops. So when I
setup a comparison rmsd with a reference structure like below:
"
from posDiffPotTools import create_PosDiffPot
refRMSD = create_PosDiffPot("refRMSD","name CA or name C or name N",
pdbFile='sura.pdb',
cmpSel="not name H*")
crossTerms.append(refRMSD)
"
the xplor-nih will reported an error:
"
File "<string>", line 2, in <module>
File "/home/bnmrc/soft/xplor-nih-2.47/python/trace.py", line 180, in run
exec cmd in dict, dict
File "<string>", line 1, in <module>
File "newRefine.py", line 70, in <module>
cmpSel="not name H*")
File "/home/bnmrc/soft/xplor-nih-2.47/python/posDiffPotTools.py", line 98, in
create_PosDiffPot
(len(selection), len(selection2)))
Exception: len(selection) [1209] != len(selection2) [1164]
PyInterp::command: error executing: >execfile('newRefine.py')<
"
I guess this may be due to the atoms number of PDB file and the atoms number
of psf file not equal. So how to solve this problem?
Second, I want to set the two domains of the crystal rigid during the
refinement. So I tried to set like this:
"
from ivm import IVM
dyn = IVM()
dyn.group(("residue 281:386","residue 28:273","residue 396:425"))
protocol.torsionTopology(dyn)
minc = IVM()
protocol.initMinimize(minc)
"
It looks like not correct because xplor report an error. So how to set the
rigid group correcltly?
Many thanks!
Xiaogang
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