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Hello Xiaogang--
> ????? I am a new user of xplor_nih. I want to refine the crystal structure of
> one protein with the RDC potentials I measured. I use the similiar script as
> I found in xplor-nih-2.22/eninput/gb1_rdc/refine.py. But I met some problems
> when I load the reference structure. I do it as:
>
> # compare atomic Cartesian rmsd with a reference structure
> #? backbone and heavy atom RMSDs will be printed in the output
> #? structure files
> #
> from posDiffPotTools import create_PosDiffPot
> refRMSD = create_PosDiffPot("refRMSD","name CA or name C or name N",
> ??????????????????????????? pdbFile="trans_xray.pdb",
> ??????????????????????????? cmpSel="not name H*")
>
> ??? But it seems xplor will quit in this point. In the output file, the
> result is :
>
> Traceback (most recent call last):
> ? File "<string>", line 2, in <module>
> ? File "/home/niuxg/xplor/xplor-nih-2.22/python/trace.py", line 180, in run
> ??? exec cmd in dict, dict
> ? File "<string>", line 1, in <module>
> ? File "refine.py", line 71, in <module>
> ??? cmpSel="not name H*")
> ? File "/home/niuxg/xplor/xplor-nih-2.22/python/posDiffPotTools.py", line 53,
> in create_PosDiffPot
> ??? (len(selection), len(selection2)))
> Exception: len(selection) [1032] != len(selection2) [1068]
> PyInterp::command: error executing: >execfile('refine.py')<
>
The file trans_xray.pdb seems to have a different sequence than that you
specified above in the script (or maybe there are missing
atoms). Anyway, for redRMSD to work you should specify an atom selection
which selects the same atoms for both sequences - something like
"(name CA or name C or name N) and resid 2:42". Also, you should
probably remove the cmpSel argument because that will also select
differing numbers of atoms.
If you can't fingure this out, you could also just remove all references
to refRMSD in the script (there is one specified in StructureLoop() at
the end of the file).
best regards--
Charles
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