Hi, sujuan, Robert provides a rich collection of pymol plugins. I myself benefit a lot from the collection.
For using msms, you can have a try of my alternative to Robert's msms_pymol.py at: http://www.biotec.tu-dresden.de/~hongboz/pymol_script/msms_pymol.py It has a graphical user interface. You can install it from PyMOL menu Plugin-->Manage Plugins-->Install. You can use the plugin to invoke MSMS for either a pdb file or a selection in PyMOL. It has been tested on PyMOL 0.98 and 1.20. best regards, Hongbo Zhu Hi Sujuan, Given that this is my script, I'll answer. :) On Tue, 11 May 2010 14:38:52 +0800 sujuan wang <wsjpy...@gmail.com> wrote: > > Hi All, > > When i run the script download from > > http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/, I issue the commond: > > calc_msms_area 2mlt-melittin, there are always something wrong as follows: > > > > CmdLoad: "D:/singapore-NTU/HU/modelling/2MLT-melittin.pdb" loaded as > > "2MLT-melittin". > > PyMOL>run C:/Program Files/DeLano Scientific/PyMOL/msms_pymol.py > > PyMOL>calc_msms_area 2MLT-melittin > > 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 281, > > 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 131, > > in calc_msms > > convert_pdb_to_xyzrn(tmp_pdb_file,tmp_xyzrn_file,atmnumbers_file) > > File "C:/Program Files/DeLano Scientific/PyMOL/msms_pymol.py", line 21, in > > convert_pdb_to_xyzrn > > lines = open(numfile).readlines() > > IOError: [Errno 2] No such file or directory: '' > > > > who can give me an example of this command? or something needed to change > > the option of script? It appears that the program is unable to find the file containing the atom type numbers. This should be a file called "atmtypenumbers" that comes with the msms program -- they are all in the one .zip file. My script attempts to find this file wherever your msms.exe program is installed. If you need further assistance, let me know. Cheers, Rob ------------------------------------------------------------------------------ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
