Dan, Please include the full PDB file in your example -- in my hands, AC5 is handled just fine so long as AC is also the element symbol...
I can't change PyMOL the way you ask without breaking other use cases -- sorry about that. However, recent version do tolerate internal spaces in a limited capacity. No plans yet to support PDBML/XML or mmCIF -- so far demand has been weak to nonexistent. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Daniel Farrell > Sent: Monday, July 18, 2005 3:46 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] spaces in atom names > > In PyMol, I am selecting a subset of atoms from a pdb file, > then saving the results to a pdb file. I'm having trouble > with spaces in ligand atom names. For example, notice that > the carbon listed below has a space as the 4th character in > the name, but after loading into pymol and then saving, the > space is now the first character. (By the way, I'm doing > "set pdb_retain_ids", "set retain_order" and "sort" before saving) > > original: > HETATM 1689 AC5 AP5 A 215 ... > > after pymol save to pdb file: > HETATM 1689 AC5 AP5 A 215 ... > > I need to preserve the original spacing and the original atom > name. I noticed in a previous email that Warren suggested > writing a python script to convert spaces to underscores > before loading in pymol. In my case, after saving the file > in pymol, I would then need to write a second script to > replace the underscores with spaces. > > Can you change pymol so that it simply stores character array elements > 12-15 as the atom name? That way, you can output the same > characters when saving. > > Also, will pymol support PDBML/XML soon? > > Thanks, > -Dan Farrell > Arizona State University > > > > > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration > Strategies from IBM. Find simple to follow Roadmaps, > straightforward articles, informative Webcasts and more! Get > everything you need to get up to speed, fast. > http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > >
