You can solve it by adding the following line in the msms_pymol.py 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.

regards,
hongbo

On 5/12/2010 1:00 PM, sujuan wang wrote:
Dear Robert,
 
I downloaded the msms  2.6.1 from http://mgltools.scripps.edu/downloads#msms 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\parser.py", line 250, in parse
    self.result=apply(layer.kw[0],layer.args,layer.kw_args)
  File "C:/Program Files/DeLano Scientific/PyMOL/msms_pymol.py", 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/msms_pymol.py", line 159, in calc_msms
    sys.exit(1)
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.
 
regards
 
Sujuan
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