<div dir="ltr">I'm using python 3.5 (Anaconda) on windows 8.1.<div><br></div><div>Regards.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Apr 8, 2017 at 8:16 PM, João Rodrigues <span dir="ltr"><<a href="mailto:j.p.g.l.m.rodrigues@gmail.com" target="_blank">j.p.g.l.m.rodrigues@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">According to the source code, that AssertionError should give you the full command: <font color="#000000"><span class="m_-5864632552327848125gmail-pl-c1" style="box-sizing:border-box;font-family:sfmono-regular,consolas,"liberation mono",menlo,courier,monospace;font-size:12px;white-space:pre-wrap">MSMS</span><span style="font-family:sfmono-regular,consolas,"liberation mono",menlo,courier,monospace;font-size:12px;white-space:pre-wrap"> </span><span class="m_-5864632552327848125gmail-pl-k" style="box-sizing:border-box;font-family:sfmono-regular,consolas,"liberation mono",menlo,courier,monospace;font-size:12px;white-space:pre-wrap">+</span><span style="font-family:sfmono-regular,consolas,"liberation mono",menlo,courier,monospace;font-size:12px;white-space:pre-wrap"> </span><span class="m_-5864632552327848125gmail-pl-s" style="box-sizing:border-box;font-family:sfmono-regular,consolas,"liberation mono",menlo,courier,monospace;font-size:12px;white-space:pre-wrap"><span class="m_-5864632552327848125gmail-pl-pds" style="box-sizing:border-box">"</span> -probe_radius 1.5 -if <span class="m_-5864632552327848125gmail-pl-c1" style="box-sizing:border-box">%s</span> -of <span class="m_-5864632552327848125gmail-pl-c1" style="box-sizing:border-box">%s</span> > <span class="m_-5864632552327848125gmail-pl-pds" style="box-sizing:border-box">"</span></span><span style="font-family:sfmono-regular,consolas,"liberation mono",menlo,courier,monospace;font-size:12px;white-space:pre-wrap"> </span><span class="m_-5864632552327848125gmail-pl-k" style="box-sizing:border-box;font-family:sfmono-regular,consolas,"liberation mono",menlo,courier,monospace;font-size:12px;white-space:pre-wrap">+</span><span style="font-family:sfmono-regular,consolas,"liberation mono",menlo,courier,monospace;font-size:12px;white-space:pre-wrap"> tempfile.mktemp()</span></font><div><font color="#000000"><span style="font-family:sfmono-regular,consolas,"liberation mono",menlo,courier,monospace;font-size:12px;white-space:pre-wrap"><br></span></font></div>What version of Python are you running? I had some issues with tempfiles recently on Windows 10, so that might be the problem here too.</div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">2017-04-08 11:09 GMT-07:00 Ahmad Abdelzaher <span dir="ltr"><<a href="mailto:underoath006@gmail.com" target="_blank">underoath006@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">Thank you for your reply. Although I'm not sure how it works because I just downloaded it for the first time, I looked it up briefly and found some commands here that I ran successfully below.<br><br><a href="http://mgl.scripps.edu/people/sanner/html/msms_man.html" target="_blank">http://mgl.scripps.edu/people/<wbr>sanner/html/msms_man.html</a><br><br>As you can see, it's version  2.6.1 and looks like it runs normally. I would appreciate if you told me how to generate a .xyzr from a .pdb though.<div><br></div><div>Regards.<br><br><br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">C:\Users\Ahmad\Documents\Spyde<wbr>r\Senior Project\Senior 2\RD>msms -if 1crn.xyzr -d<br>e 3.0 -prob 1.4 -of myset<br>MSMS 2.6.1 started on Local PC<br>Copyright M.F. Sanner (1994)<br>Compilation flags<br>INPUT  1crn.xyzr 327 spheres 0 collision only, radii  1.400 to  2.000<br>PARAM  Probe_radius  1.400 density  3.000 hdensity  3.000<br>ANALYTICAL SURFACE AREA :<br>    Comp. probe_radius,   reent,    toric,   contact    SES       SAS<br>      0       1.400     459.878   904.748   977.802  2342.427  3030.759<br>NUMERICAL VOLUMES AND AREA<br>    Comp. probe_radius SES_volume SES_area)<br>       0      1.40     5150.775   2306.089<br>    Total ses_volume:  5150.775<br>MSMS terminated normally<br>C:\Users\Ahmad\Documents\Spyde<wbr>r\Senior Project\Senior 2\RD></blockquote></div></div><div class="m_-5864632552327848125HOEnZb"><div class="m_-5864632552327848125h5"><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Apr 8, 2017 at 7:55 PM, João Rodrigues <span dir="ltr"><<a href="mailto:j.p.g.l.m.rodrigues@gmail.com" target="_blank">j.p.g.l.m.rodrigues@gmail.com</a><wbr>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Ahmad,<div><br></div><div>What version of msms are you using? Can you run the program outside of Biopython to obtain the surface file?</div><div><br></div><div>Cheers,</div><div><br></div><div>João</div></div>
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