[Biopython] ResidueDepth msms.exe has stopped working

[Ahmad Abdelzaher]

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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