[Biopython] Problem with ResidueDepth class

[Carlos Henrique]

Hi Lenna,
Thank you so much for your quick answer!

And that was exactly the problem here. I extracted only the *msms*,
*pdb_to_xyrz* and *pdb_to_xyrzn* files to my* /usr/local/bin*.

I just moved the *atmtypenumbers* and changed the path in *pdb_to_xyrn* and
worked like a charm.
:)
Thanks once more.

Cheers,

Carlos

2015-11-09 20:03 GMT-02:00 Lenna Peterson <arklenna at gmail.com>:

> Hi Carlos,
>
> I am able to get ResidueDepth and surface from 1yrk (although I notice
> neither function is covered by the test suite, perhaps due to the soft
> dependencies).
>
> The error means that pdb_to_xyzr is not able to find an entry for a water
> oxygen in the file "atmtypenumbers".
>
> In pdb_to_xyzr, the path to atmtypenumbers is specified relatively, so my
> suspicion is that you're not running it from the directory where
> atmtypenumbers is located and it's not being found at all. If that is the
> case, I would recommend editing pdb_to_xyzr to specify an absolute path
> (e.g. change the line 'numfile = "./atmtypenumbers"' to something like
> 'numfile = /home/carlos/...').
>
> Please let me know if that fixes your problem.
>
> Cheers,
>
> Lenna
>
> On Mon, Nov 9, 2015 at 3:58 PM, Carlos Henrique <carlosmr12 at gmail.com>
> wrote:
>
>> Hello everyone,
>> I have been struggling with the calculation of Residue depth using the
>> class ResidueDepth as mentioned in [1
>> <http://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ#How_do_I_calculate_residue_depth.3F>
>> ].
>> I already set everything up and installed the msms from [2
>> <http://mgltools.scripps.edu/downloads#msms>].
>> However, I cannot make it run as it should. At first I thought it could
>> be a problem with my .pdb files, but I tested with 3 different files
>> downloaded directly from the protein data bank (1YRK, 1B4F, 1U46) and I
>> keep getting the same error message which is something like this:
>>
>> A bunch of this:
>> pdb_to_xyzr: error, file 1YRK.pdb line 1687 residue   37 atom pattern HOH
>> O was not found in ./atmtypenumbers
>> pdb_to_xyzr: error, file 1YRK.pdb line 1688 residue   38 atom pattern HOH
>> O was not found in ./atmtypenumbers
>> pdb_to_xyzr: error, file 1YRK.pdb line 1689 residue   39 atom pattern HOH
>> O was not found in ./atmtypenumbers
>> pdb_to_xyzr: error, file 1YRK.pdb line 1690 residue   40 atom pattern HOH
>> O was not found in ./atmtypenumbers
>> pdb_to_xyzr: error, file 1YRK.pdb line 1691 residue   41 atom pattern HOH
>> O was not found in ./atmtypenumbers
>> pdb_to_xyzr: error, file 1YRK.pdb line 1692 residue   42 atom pattern HOH
>> O was not found in ./atmtypenumbers
>>
>> and the traceback error message right after:
>> Traceback (most recent call last):
>>   File "generate_measurements.py", line 82, in <module>
>>     rd = ResidueDepth(struct[0], '1YRK.pdb')
>>   File
>> "/home/carlos/.virtualenvs/pdb/local/lib/python2.7/site-packages/Bio/PDB/ResidueDepth.py",
>> line 144, in __init__
>>     surface=get_surface(pdb_file)
>>   File
>> "/home/carlos/.virtualenvs/pdb/local/lib/python2.7/site-packages/Bio/PDB/ResidueDepth.py",
>> line 90, in get_surface
>>     "Failed to generate surface file using command:\n%s" % make_surface
>> AssertionError: Failed to generate surface file using command:
>> msms -probe_radius 1.5 -if /tmp/tmpwodW16 -of /tmp/tmpCbMTwN >
>> /tmp/tmprkvaQv
>>
>> I have been trying to solve this since yesterday in vain. Does anyone
>> have any clue or maybe I can get the residue depth using something else?
>>
>> Cheers,
>>
>> [1]
>> http://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ#How_do_I_calculate_residue_depth.3F
>> [2] http://mgltools.scripps.edu/downloads#msms
>>
>> --
>> Carlos Rodrigues
>>
>>
>> _______________________________________________
>> Biopython mailing list  -  Biopython at mailman.open-bio.org
>> http://mailman.open-bio.org/mailman/listinfo/biopython
>>
>
>


-- 
Carlos Rodrigues
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