[Biopython] ResidueDepth msms.exe has stopped working

[Ahmad Abdelzaher]

I have no idea I bypasses it. I just simply ran the code in Spyder which
generated the error.

Regards.

On Sat, Apr 8, 2017 at 8:28 PM, João Rodrigues <
j.p.g.l.m.rodrigues at gmail.com> wrote:

> So, I run into a different problem here (windows 10, python 3.6).
> Apparently, the ResidueDepth code depends on pdb_to_xyzr, which is a BASH
> script that cannot run on windows. It seems to be a simple lookup table
> though, so we might be able to re-write it in Python. How did you bypass
> this to get to your error?
>
>
>
> 2017-04-08 11:18 GMT-07:00 Ahmad Abdelzaher <underoath006 at gmail.com>:
>
>> I'm using python 3.5 (Anaconda) on windows 8.1.
>>
>> Regards.
>>
>> On Sat, Apr 8, 2017 at 8:16 PM, João Rodrigues <
>> j.p.g.l.m.rodrigues at gmail.com> wrote:
>>
>>> According to the source code, that AssertionError should give you the
>>> full command: MSMS + " -probe_radius 1.5 -if %s -of %s > " +
>>> tempfile.mktemp()
>>>
>>> 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.
>>>
>>> 2017-04-08 11:09 GMT-07:00 Ahmad Abdelzaher <underoath006 at gmail.com>:
>>>
>>>> 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.
>>>>
>>>> http://mgl.scripps.edu/people/sanner/html/msms_man.html
>>>>
>>>> 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.
>>>>
>>>> Regards.
>>>>
>>>>
>>>> C:\Users\Ahmad\Documents\Spyder\Senior Project\Senior 2\RD>msms -if
>>>>> 1crn.xyzr -d
>>>>> e 3.0 -prob 1.4 -of myset
>>>>> MSMS 2.6.1 started on Local PC
>>>>> Copyright M.F. Sanner (1994)
>>>>> Compilation flags
>>>>> INPUT  1crn.xyzr 327 spheres 0 collision only, radii  1.400 to  2.000
>>>>> PARAM  Probe_radius  1.400 density  3.000 hdensity  3.000
>>>>> ANALYTICAL SURFACE AREA :
>>>>>     Comp. probe_radius,   reent,    toric,   contact    SES       SAS
>>>>>       0       1.400     459.878   904.748   977.802  2342.427  3030.759
>>>>> NUMERICAL VOLUMES AND AREA
>>>>>     Comp. probe_radius SES_volume SES_area)
>>>>>        0      1.40     5150.775   2306.089
>>>>>     Total ses_volume:  5150.775
>>>>> MSMS terminated normally
>>>>> C:\Users\Ahmad\Documents\Spyder\Senior Project\Senior 2\RD>
>>>>
>>>>
>>>> On Sat, Apr 8, 2017 at 7:55 PM, João Rodrigues <
>>>> j.p.g.l.m.rodrigues at gmail.com> wrote:
>>>>
>>>>> Hi Ahmad,
>>>>>
>>>>> What version of msms are you using? Can you run the program outside of
>>>>> Biopython to obtain the surface file?
>>>>>
>>>>> Cheers,
>>>>>
>>>>> João
>>>>>
>>>>
>>>>
>>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20170408/78def8ca/attachment.html>