Hello Xiaogang--
> 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?
You have correctly identified the problem. To fix it, you need to omit
the missing residues from the atom selection. So, instead of
"name CA C N" (equivalent to what you have above), you will want
"name CA C N and not resid r1 r2:r3", where r1 represents an
individual residue number, and r2:r3 represents a range including r2,
r2+1, ... r3.
>
> 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"))
This should be
ranges=["281:386","28:273","396:425"]
for range in ranges:
dyn.group("residue "+range)
i.e. each rigid body requires its own group() invocation.
best regards--
Charles
########################################################################
To unsubscribe from the XPLOR-NIH list, click the following link:
http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
