>
> Hello Charles and John,
>
> I ran the program with the -quick flag. So I only expected to see the first
> 36 residues. I also checked the disk quota and there is plenty of disk space
> so that shouldn't be a problem. I made a truncated version of the
> cvn_reference.pdb ending at LEU 36 O. Then I modified refine.py line 84 to
> load the truncated file. Now it tells me the selections are of unequal
> length, in regards to non-H atoms (See output below). Both files contain 518
> atoms at the terminal O, so without looking over each atom I would assume
> the number of non-H atoms is the same.
>
> Thanks,
> CDW
>
> loading pdb file: ./cvn_reference_trunc.pdb [psf]PDBTool:read: atom not
> found in structure: LEU 36 O
> matchInexactAtomEntry: matching entry 36 O to atom 36 OT1
> initCoords: still 3 unknown atomic coordinates
> [coords]
> cmpSel: selections are of unequal length:
> 0: not name H* -- 265 atoms
> 1: not name H* -- 266 atoms
> Traceback (most recent call last):
> File "<string>", line 2, in <module>
> File "/work/chem_eng3/OLD/cdw/xplor-nih-2.23/python/trace.py", line 180,
> in run
> exec cmd in dict, dict
> File "<string>", line 1, in <module>
> File "refine.py", line 85, in <module>
> cmpSel="not name H*")
> File "/work/chem_eng3/OLD/cdw/xplor-nih-2.23/python/posDiffPotTools.py",
> line 83, in create_PosDiffPot
> raise Exception("cmpSel: selections are of unequal length")
> Exception: cmpSel: selections are of unequal length
> PyInterp::command: error executing: >execfile('refine.py')<
>
>
> On Tue, Jun 9, 2009 at 5:03 PM, John Kuszewski <john.kuszewski at
> gmail.com>wrote:
>
>>
>> On Jun 9, 2009, at 5:04 PM, Charles at schwieters.org wrote:
>>
>> -----BEGIN PGP SIGNED MESSAGE-----
>>> Hash: SHA1
>>>
>>>
>>> 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
>>> -----BEGIN PGP SIGNATURE-----
>>> Version: GnuPG v1.4.9 (GNU/Linux)
>>> Comment: Processed by Mailcrypt 3.5.8+ <
>>> http://mailcrypt.sourceforge.net/>
>>>
>>> iEYEARECAAYFAkouzmgACgkQPK2zrJwS/lYh8ACfUITwPhuJOD+FfpPzPhqdQJ6g
>>> Ca0An2lp68mscfzDtgmdFAFU1tSCwHG3
>>> =WO7d
>>> -----END PGP SIGNATURE-----
>>>
>>> _______________________________________________
>>> Xplor-nih mailing list
>>> Xplor-nih at nmr.cit.nih.gov
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>>>
>>
>>
>
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