Hi Anasuya, instead of "python" you must type "run":
PyMOL>run findSurfaceResidues.py PyMOL>findSurfaceResidues doShow=True, cutoff=2.5 That's all. Quick explanation what happend in your case: With the "python" command you start a multi-line python block in the PyMOL command line interpreter, which will only be executed once you type "python end". Therefore nothing happend. Cheers, Thomas Anasuya Dighe wrote, On 05/05/12 13:08: > Hi Pymol Users, > > I was trying to use the findSurfaceResidues.py script listed on PyMOLwiki > (http://www.pymolwiki.org/index.php/FindSurfaceResidues), to find out which > residues which are present on the surface of the protein. > > These are the steps I have followed: > 1) Made a file called findSurfaceResidues.py [with the code as mentioned on > PyMOlwiki], in my /home/anasuya/Desktop folder. > 2) Opened PyMOL from my Desktop folder. > 3) In the command line window of PyMOL, I typed in: python > findSurfaceResidues.py > 4) Next, as mentioned on the PyMOLwiki page, I typed: findSurface residues > doShow=True > 5) And finally I typed : findSurfaceResidues doShow=True, cutoff=2.0 > > However, I am not able to visualize anything. > On the command line window in PyMOL, I see the following: > > PyMOL>python findSurfaceResidues.py > PyMOL>findSurface residues doShow=True > 1:findSurface residues doShow=True > PyMOL>findSurfaceResidues doShow=True, cutoff=2.5 > 2:findSurfaceResidues doShow=True, cutoff=2.5 > > Please tell me what seems to be wrong with my procedure. > > Thanks, > - Anasuya -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ 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
