Hello, > I am quite new to python and more specifically to PYTHON ,PYMOL interface > hence I urgently need a help from you.
Welcome! This list has about 1500 people on it and is accepting of new users. A couple hints to get you started. First, you can type "help commandName" in PyMOL to help on a given command. You can also type "help" to get general help. Next, we have a community-editable wiki, the PyMOLWiki (http://pymolwiki.org) that has thousands of pages of information to get you up to speed. > I simple need to calculate the RMSD between two pdb files and use that rmsd > for further programming but somehow I can not figure how to do it > This is what I have written till now > [codes are in bold] > > from pymol import cmd > cmd.load("pdb%04d.pdb"%ener1) > cmd.load("pdb%04d.pdb"%ener2) > This I believe should just load in the PDBs through PYMOL [both these pdbs > are in the same directory] > rms=cmd.fit(pdb ???? ) so I do not know how to get the RMSD using this > function ( I need for CA atoms only) Here, cmd.fit is expecting two protein selections to fit. So, we can give it something like: # fit protein pdb0001 to pdb0002 v = cmd.fit("pdb0001", "pdb0002") # print the RMS print v But as you stated you only want alpha carbons you can restrict the selection of each protein to just alpha carbons using the selection syntax "name CA": v = cmd.fit("pdb0001 and name CA", "pdb0002 and name CA") print v To learn more about PyMOL selections please see (http://www.pymolwiki.org/index.php/Category:Selecting). > This is the only part where I am getting jammed . I only need the RMSD > values between the structures(without any changes to the structures) If you want PyMOL to do the calculation, but leave the structures untouched use "cmd.rms" instead of "cmd.fit". They both have a similar syntax. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev _______________________________________________ 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
