[Biopython] ResidueDepth msms.exe has stopped working

[Ahmad Abdelzaher]

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
>>>
>>
>>
>
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