Hi Ben, > Basically, I have three separate saved PyMOL sessions (*.pse files). Each of > these has a bunch of named selections, which it took me several hours to > define properly. I would like to superimpose the proteins in the different > sessions with each other, and I guess that means they have to be in the same > session. But exporting the coordinates from one session and re-importing them > - or just going back to the original PDB files - will necessarily not include > the named selections. > > So, is there a way to export named selections from one session and import > them into another? Or, failing that, at least a way to spit out a list of the > atoms comprising any given selection in one session, and then use that list > to define a corresponding selection in another session?
Wouldn't it be nice to be able to combine sessions? We will work on that. In the meantime, at least three options come to mind. I'll describe the two easiest which involve saving the selections to disk. You will then have to reload the files and do your alignments. First save the named selections as PDBs. Then load the PDBs into PyMOL and do your alignments. What's nice about this is you can load the sub-structures from the named selections and the full structures, too. After aligning the sub-structures use their TTT matrices to transform the full structurs. Here's how, # save myNamedSelection to the file newObj.pdb save newObj.pdb, myNamedSelection Do this for each selection in each session, saving each to a different PDB file. Now, restart PyMOL and load in the new substructures from the PDBs you just created. Do the alignments. Load the full structures if you want, too. If you want to transform "fullObject" onto the aligned "subStructureObject" then do, # copy the TTT matrix from subStructureObj onto fullObject use "matrix_copy", matrix_copy subStructureObj, fullObject For more help, see the create and matrix_copy commands on the PyMOLWiki: http://www.pymolwiki.org/index.php/Create http://www.pymolwiki.org/index.php/Matrix_copy Other possible methods include: * writing pickled chempy objects to disk * iterating over the selection and writing atom info to disk but I prefer the first. Good luck. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ FREE DOWNLOAD - uberSVN with Social Coding for Subversion. Subversion made easy with a complete admin console. Easy to use, easy to manage, easy to install, easy to extend. Get a Free download of the new open ALM Subversion platform now. http://p.sf.net/sfu/wandisco-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
