[Biopython] ResidueDepth msms.exe has stopped working

[João Rodrigues]

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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