<div dir="ltr">Hi Lenna,<div>Thank you so much for your quick answer!</div><div><br></div><div>And that was exactly the problem here. I extracted only the <i>msms</i>, <i>pdb_to_xyrz</i> and <i>pdb_to_xyrzn</i> files to my<i> /usr/local/bin</i>.</div><div><br></div><div>I just moved the <span style="font-size:12.8px"><i>atmtypenumbers</i> and changed the path in <i>pdb_to_xyrn</i> and worked like a charm. </span></div><div><span style="font-size:12.8px">:)</span></div><div><span style="font-size:12.8px">Thanks once more.</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">Cheers,</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">Carlos</span></div></div><div class="gmail_extra"><br><div class="gmail_quote">2015-11-09 20:03 GMT-02:00 Lenna Peterson <span dir="ltr"><<a href="mailto:arklenna@gmail.com" target="_blank">arklenna@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Carlos,<div><br></div><div>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). </div><div><br></div><div>The error means that pdb_to_xyzr is not able to find an entry for a water oxygen in the file "atmtypenumbers". </div><div><br></div><div>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/...').</div><div><br></div><div>Please let me know if that fixes your problem.</div><div><br></div><div>Cheers,</div><div><br></div><div>Lenna</div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="h5">On Mon, Nov 9, 2015 at 3:58 PM, Carlos Henrique <span dir="ltr"><<a href="mailto:carlosmr12@gmail.com" target="_blank">carlosmr12@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div dir="ltr"><span style="font-size:12.8px">Hello everyone,</span><div style="font-size:12.8px">I have been struggling with the calculation of Residue depth using the class <span style="color:rgb(0,0,0);line-height:1.3em;background-color:rgb(249,249,249)">ResidueDepth as mentioned in [<a href="http://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ#How_do_I_calculate_residue_depth.3F" target="_blank">1</a>].</span></div><div style="font-size:12.8px"><font color="#000000"><span style="line-height:16.9px">I already set everything up and installed the msms from [<a href="http://mgltools.scripps.edu/downloads#msms" target="_blank">2</a>]. </span></font></div><div style="font-size:12.8px"><font color="#000000"><span style="line-height:16.9px">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:</span></font></div><div style="font-size:12.8px"><font color="#000000"><span style="line-height:16.9px"><br></span></font></div><div style="font-size:12.8px"><font color="#000000"><span style="line-height:16.9px">A bunch of this:</span></font></div><div style="font-size:12.8px"><font color="#000000"><div><span style="line-height:16.9px">pdb_to_xyzr: error, file 1YRK.pdb line 1687 residue 37 atom pattern HOH O was not found in ./atmtypenumbers</span></div><div><span style="line-height:16.9px">pdb_to_xyzr: error, file 1YRK.pdb line 1688 residue 38 atom pattern HOH O was not found in ./atmtypenumbers</span></div><div><span style="line-height:16.9px">pdb_to_xyzr: error, file 1YRK.pdb line 1689 residue 39 atom pattern HOH O was not found in ./atmtypenumbers</span></div><div><span style="line-height:16.9px">pdb_to_xyzr: error, file 1YRK.pdb line 1690 residue 40 atom pattern HOH O was not found in ./atmtypenumbers</span></div><div><span style="line-height:16.9px">pdb_to_xyzr: error, file 1YRK.pdb line 1691 residue 41 atom pattern HOH O was not found in ./atmtypenumbers</span></div><div><span style="line-height:16.9px">pdb_to_xyzr: error, file 1YRK.pdb line 1692 residue 42 atom pattern HOH O was not found in ./atmtypenumbers</span></div><div style="line-height:16.9px"><br></div><div style="line-height:16.9px">and the traceback error message right after:</div><div style="line-height:16.9px"><div style="line-height:16.9px">Traceback (most recent call last):</div><div style="line-height:16.9px"> File "generate_measurements.py", line 82, in <module></div><div style="line-height:16.9px"> rd = ResidueDepth(struct[0], '1YRK.pdb')</div><div style="line-height:16.9px"> File "/home/carlos/.virtualenvs/pdb/local/lib/python2.7/site-packages/Bio/PDB/ResidueDepth.py", line 144, in __init__</div><div style="line-height:16.9px"> surface=get_surface(pdb_file)</div><div style="line-height:16.9px"> File "/home/carlos/.virtualenvs/pdb/local/lib/python2.7/site-packages/Bio/PDB/ResidueDepth.py", line 90, in get_surface</div><div style="line-height:16.9px"> "Failed to generate surface file using command:\n%s" % make_surface</div><div style="line-height:16.9px">AssertionError: Failed to generate surface file using command:</div><div style="line-height:16.9px">msms -probe_radius 1.5 -if /tmp/tmpwodW16 -of /tmp/tmpCbMTwN > /tmp/tmprkvaQv</div><div><br></div><div>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?</div><div><br></div><div>Cheers,</div></div></font></div><div style="font-size:12.8px"><font color="#000000"><span style="line-height:16.9px"><br></span></font></div><div style="font-size:12.8px"><font color="#000000"><span style="line-height:16.9px">[1] <a href="http://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ#How_do_I_calculate_residue_depth.3F" target="_blank">http://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ#How_do_I_calculate_residue_depth.3F</a></span></font></div><div style="font-size:12.8px"><font color="#000000"><span style="line-height:16.9px">[2] </span></font><a href="http://mgltools.scripps.edu/downloads#msms" style="color:rgb(52,101,164)" target="_blank">http://mgltools.scripps.edu/downloads#msms</a></div><span><font color="#888888"><div><br></div>-- <br><div><div dir="ltr">Carlos Rodrigues<div><div><br></div></div></div></div>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr">Carlos Rodrigues<div><div><br></div></div></div></div>
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