[Biopython] ResidueDepth msms.exe has stopped working

[João Rodrigues]

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
>>>>
>>>
>>>
>>
>
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