On Jun 9, 2009, at 5:04 PM, Charles at schwieters.org wrote:
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> Hello Chris--
>
>> So now I'm trying to finish running the pasd/cvn tutorial. I've
>> submitted the
>> job using the quick flag and everything runs well until the
>> refine.py command
>> is implemented in the runPASDquick script,
>
>>
>> xplor -quick -py refine.py -parallel -machines ${PBS_NODEFILE} >
>> refine.py.out
>>
>> At this point my job terminates. I checked the refine.py.out file
>> which
>> contained this,
>>
>
>> refine.py(59): protocol.loadPDB("./cvn_pass3_avg.pdb")
>> loading pdb file: ./cvn_pass3_avg.pdb [psf]PDBTool:read: atom not
>> found in
>> structure: LEU 36 O
>> matchInexactAtomEntry: matching entry 36 O to atom 36 OT1
>>
>
> It seems like the input file (cvn_pass3_avg.pdb) was truncated at
> resid
> 36. Did you run out of disk space?
Or did you run the scripts with the -quick flag, which (at least in
previous versions) only calculates the structure of the first 36
residues?
--JK
>
>
>> refine.py(83): refRMSD = create_PosDiffPot("refRMSD","name CA or
>> name C or name
>> N",
>> refine.py(84): pdbFile='./
>> cvn_reference.pdb',
>> refine.py(85): cmpSel="not name H*")
>
>> Exception: len(selection) [108] != len(selection2) [303]
>
> This is due to the size difference between the input and reference
> structures.
>
> best regards--
> Charles
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