[Biopython] ResidueDepth msms.exe has stopped working

[João Rodrigues]

OK. I'll look into this, thanks for raising this.

2017-04-08 11:31 GMT-07:00 Ahmad Abdelzaher <underoath006 at gmail.com>:

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