I'm not sure how version-dependent this is, but setting connect_mode to 1 before loading the PDB should disable distance-based connectivity determination.
set connect_mode, 1 load CONECT_only_pdb.pdb -- 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 > Eric Zollars > Sent: Thursday, November 17, 2005 5:36 PM > To: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] displaying protein with propeptide > > Is there a similar command to force PyMOL to use only CONECT > lines in the pdb file instead of generating connectivity by distance? > > Eric > > Warren DeLano wrote: > > 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 > >> > >> > >> > >> > > > > > > > > ------------------------------------------------------- > > 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 > > > ------------------------------------------------------- > 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 > > > >
