You can solve it by adding the following line in the you downloaded from Robert's page to line 133, right before msms_cmd is defined.

    if msms_path.startswith('C:/'): msms_path = '\"%s\"' % (msms_path,)

Basically, your problem was caused by the whitespace in the path to the MSMS executable file in Windows systems. By adding quotes to the full path solves the problem.


On 5/12/2010 1:00 PM, sujuan wang wrote:
Dear Robert,
I downloaded the msms  2.6.1 from and installed into C:\Program Files\MSMS. But there are still something wrong after running the script:
There seems to be a problem with the msms output
Traceback (most recent call last):
  File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\", line 250, in parse
  File "C:/Program Files/DeLano Scientific/PyMOL/", line 282, in calc_msms_area
    volume,area_dict,tmp_msms_vert_file,tmp_msms_face_file = calc_msms(object_name,probe,density,keep,debug)
  File "C:/Program Files/DeLano Scientific/PyMOL/", line 159, in calc_msms
SystemExit: 1
My pymol version is 1.1r1 with python 2.4.2 (#67, Sep 28 2005, 12:41:11) [MSC v.1310 32 bit (Intel)]
As a beginner of pymol, thank you for your kindly help.
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