[Biopython] Problem with ResidueDepth class

[Lenna Peterson]

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
>
>
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> Biopython mailing list  -  Biopython at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython
>
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