A quick fix is to use the "retain_order" setting. set retain_order
which will force PyMOL to honor the order of ATOMs in the PDB file over the numeric ordering of residue identifiers. 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 > Joel Tyndall > Sent: Thursday, November 17, 2005 12:15 PM > To: Anne Mølgaard; pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] displaying protein with propeptide > > Hi Ann, > > I would change the chain id of the propeptide in a text > editor, to say P and remove the P from after the residue numbers. > > J > > Anne Mølgaard wrote: > > >Hi, > > > >I am having problems displaying proteins with unusual residue > >numbering, such as proteins with propeptides. An example is > 1cs8, which > >starts off like > >this: > > > >ATOM 1 N SER A 1P -32.762 23.978 22.929 0.00 34.26 > >N > >ATOM 2 CA SER A 1P -32.360 24.645 21.660 0.00 34.08 > >C > >ATOM 3 C SER A 1P -32.303 26.162 21.821 0.00 33.91 > >C > >ATOM 4 O SER A 1P -32.838 26.712 22.786 0.00 33.82 > >O > >ATOM 5 CB SER A 1P -33.338 24.274 20.541 0.00 34.28 > >C > >ATOM 6 OG SER A 1P -34.684 24.406 20.971 0.00 34.36 > >O > >. > >. > >. > >And later on comes the sequence corresponding to the mature protein: > > > >ATOM 1060 N ALA A 1 11.470 66.852 16.148 1.00 22.69 > >N > >ATOM 1061 CA ALA A 1 11.282 65.561 15.491 1.00 20.80 > >C > >ATOM 1062 C ALA A 1 10.621 65.677 14.113 1.00 20.33 > >C > >ATOM 1063 O ALA A 1 9.920 66.649 13.835 1.00 18.43 > >O > >ATOM 1064 CB ALA A 1 10.451 64.636 16.393 1.00 19.50 > >C > >Etc. > > > >If I open 1cs8 with PyMol, I can see everything in the "lines", > >"sticks" and "surface" representation, but in ribbon or cartoon mode > >only part of the protein is shown. What do I have to do to > show the whole sequence? > > > >How do I select residues with a "P" appended to the residue > number? If > >I say "select resi 1P-5P" I get both 1P-5P and 1-5. > > > >Any help will be appreciated! (I am using PyMol version 0.98 > for Windows). > > > >- Anne > > > >-------------------------------------------- > >Anne Mølgaard, Ph.D. > >Center for Biological Sequence Analysis BioCentrum-DTU, Building 208 > >DK-2800 Lyngby > > > >Email: a...@cbs.dtu.dk > >Phone: (+45)4525 2472 > >-------------------------------------------- > > > > > > > > > >------------------------------------------------------- > >This SF.Net email is sponsored by the JBoss Inc. Get Certified Today > >Register for a JBoss Training Course. Free Certification Exam > >for All Training Attendees Through End of 2005. For more info visit: > >http://ads.osdn.com/?ad_idv28&alloc_id845&op=click > >_______________________________________________ > >PyMOL-users mailing list > >PyMOL-users@lists.sourceforge.net > >https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > > -- > Joel Tyndall, PhD > > Lecturer > National School of Pharmacy > University of Otago > PO Box 913 Dunedin > New Zealand > > Pukenga > Te Kura Taiwhanga Putaiao > Te Whare Wananga o Otago > Pouaka Poutapeta 913 Otepoti > Aotearoa > > Ph / Waea +64 3 4797293 > Fax / Waeawhakaahua +64 3 4797034 > > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. Get Certified Today > Register for a JBoss Training Course. Free Certification Exam > for All Training Attendees Through End of 2005. For more info visit: > http://ads.osdn.com/?ad_idv28&alloc_id845&op=ick > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > >
