Anne, > "select resi 1P-5P" still gives me both 1-5 and 1P-5P. > However, "select resi 1P+2P+3P+4P+5P" gives me what I want.
Say you have residues 36, 37A, 37B, and 38, and you tell PyMOL you wish to select residues in the range 36-38. Naturally, you'd want 37A and 37B included in that. It is this behavior that gives rise to the selection behavior you've noted above, wherein residue insertion codes are effectively ignored inside numerical ranges. In PyMOL, ranges are defined numerically for reasons of performance. Defining them based on peptide connectivity would be orders of magnitude slower. Defining them based on their input file order could give okay performance, but the concept of input order is not always valid given that molecules are graphs not lists. I agree though, that it would be nice to equip PyMOL with these alternate ranging concepts -- ideas for the future. Fortunately, there is another workaround: segment identifiers. With wildcard selection in PyMOL beta builds, you can do something like this: alter resi *B, segi='SEG1' alter not resi *B, segi='SEG2' Now you could use ranges without trouble, leaving your chain IDs unperturbed. select segi SEG1 and resi 1-5 or more concisely: select SEG1//1-5/ as distinct from select SEG2//1-5/ > but many PDB files have insertions which are numbered with "A"s and "B"s > after the residue number, As for insertion codes that appear at the proper location in sequence (NOT the case with pathological PDB 1cs8), recent PyMOL betas handle such situations automatically and will draw connected cartoons. 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 > Anne Mølgaard > Sent: Friday, November 18, 2005 12:47 AM > To: pymol-users@lists.sourceforge.net > Subject: RE: [PyMOL] displaying protein with propeptide > > Thanks for the comments. The "retain_order" setting solves > the problem with cartoons and ribbons, but there is still a > small problem with selection of these residues. "select resi > 1P-5P" still gives me both 1-5 and 1P-5P. > However, "select resi 1P+2P+3P+4P+5P" gives me what I want. > > I don't really want to change the chain ID in the PDB file. > It makes sort of sense in the case of a propeptide (although > it is covalently linked to the mature protein, so it is > really only one chain), but many PDB files have insertions > which are numbered with "A"s and "B"s after the residue > number, and in those cases it really doesn't make sense to > change the chain ID. For an example, see 1cgh below. > > Thanks for your help! > > - Anne > > ATOM 213 OE1 GLN A 36 8.532 36.321 21.186 0.00 25.64 > O > ATOM 214 NE2 GLN A 36 7.727 36.504 19.104 0.00 25.95 > N > ATOM 215 H GLN A 36 8.523 31.138 18.943 0.00 20.00 > H > ATOM 216 1HE2 GLN A 36 7.711 37.475 19.199 0.00 20.00 > H > ATOM 217 2HE2 GLN A 36 7.446 36.036 18.288 0.00 20.00 > H > ATOM 218 N SER A 36A 4.622 31.686 20.477 0.00 27.20 > N > ATOM 219 CA SER A 36A 3.235 31.238 20.479 0.00 28.70 > C > ATOM 220 C SER A 36A 2.315 32.417 20.162 0.00 29.65 > C > ATOM 221 O SER A 36A 2.664 33.569 20.429 0.00 30.07 > O > ATOM 222 CB SER A 36A 2.878 30.647 21.845 0.00 28.71 > C > ATOM 223 OG SER A 36A 3.565 29.428 22.077 0.00 29.15 > O > ATOM 224 H SER A 36A 5.000 32.029 21.306 0.00 20.00 > H > ATOM 225 HG SER A 36A 4.526 29.487 22.051 0.00 20.00 > H > ATOM 226 N PRO A 36B 1.124 32.146 19.598 0.00 30.41 > N > ATOM 227 CA PRO A 36B 0.593 30.825 19.240 0.00 31.02 > C > ATOM 228 C PRO A 36B 1.323 30.182 18.061 0.00 31.62 > C > ATOM 229 O PRO A 36B 2.169 30.814 17.426 0.00 31.58 > O > ATOM 230 CB PRO A 36B -0.867 31.125 18.914 0.00 30.83 > C > ATOM 231 CG PRO A 36B -0.789 32.492 18.316 0.00 30.95 > C > ATOM 232 CD PRO A 36B 0.147 33.200 19.269 0.00 30.41 > C > ATOM 233 N ALA A 37 0.991 28.925 17.777 0.00 32.51 > N > ATOM 234 CA ALA A 37 1.608 28.191 16.677 0.00 33.56 > C > > -------------------------------------------- > 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 > -------------------------------------------- > > -----Original Message----- > From: Warren DeLano [mailto:war...@delsci.com] > Sent: 18. november 2005 02:28 > To: Joel Tyndall; Anne Mølgaard; pymol-users@lists.sourceforge.net > Subject: RE: [PyMOL] displaying protein with propeptide > > 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=ick > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > >
