Whoops, I misread my own code: In fact, PyMOL already supports 5-character residue identifiers! Here's how you use them, assuming a PDB file where the resi field spills into chain:
load your_file.pdb alter all, resi=chain+resi sort # and off you go indicate resi 10000: zoom resi 10123 Cheers, Warren > -----Original Message----- > From: Warren DeLano > Sent: Tuesday, June 09, 2009 12:26 PM > To: ABEL Stephane 175950 > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] How to plot residu with a number > 9999 > > Stephane, > > Okay, I see -- you're just spilling the top digit into the > chain id. So for residue 10123, you can issue a selection like: > > zoom chain 1 and resi 0123 > > Looking over the code, I note that PyMOL has a hardcoded resi > field of just four characters plus a null. Given how C > compilers pack structs, I suspect we could extend that to 7 > characters plus a null without adversely impacting PyMOL's > memory use characteristics... > > Cheers, > Warren > > > -----Original Message----- > > From: ABEL Stephane 175950 [mailto:stephane.a...@cea.fr] > > Sent: Tuesday, June 09, 2009 12:34 AM > > To: Warren DeLano > > Subject: RE : [PyMOL] How to plot residu with a number > 9999 > > > > Warren, > > > > Thank you for your response > > > > Indeed, you are right and this is a well known limitation > of the pdb > > format. But as you can see with the file i join in this message > > obtained from a molecular dynamics software, you can also use the > > field 22 - 26 to extend the resSeq to 99999 and this with > pymol and rasmol. > > > > > > > > ------------------------------ > > Stéphane Abel, PhD > > CEA Saclay DSV/IBITEC-S/SB2SM > > 91191 Saclay, FRANCE > > website: http://www.st-abel.com > > ------------------------------ > > > > > > > > -------- Message d'origine-------- > > De: Warren DeLano [mailto:war...@delsci.com] > > Date: mar. 09/06/2009 02:01 > > À: ABEL Stephane 175950; pymol-users@lists.sourceforge.net > Objet : RE: > > [PyMOL] How to plot residu with a number > 9999 > > > > Stephane, > > > > As per http://www.wwpdb.org/documentation/format32/sect9.html , the > > PDB residue identifier field is only four characters wide. > > > > So how could you possibly have a PDB file with residue identifiers > > larger than 9999? > > > > Cheers, > > Warren > > > > > -----Original Message----- > > > From: Stephane Abel [mailto:stephane.a...@cea.fr] > > > Sent: Monday, June 08, 2009 7:30 AM > > > To: pymol-users@lists.sourceforge.net > > > Subject: [PyMOL] How to plot residu with a number > 9999 > > > > > > Hi pymol users > > > > > > > > > It seems that the command select, residue xxx to plot residue xxx > > where > > > xxx is greater than 9999 does not work in pymol version 0.99rc6 > > > > > > > > > Indeed for a pdb file with ~ 13800 residue, if i use the command: > > > > > > > > > select water1846, residue 1846 -> the water molecule with the > > > residue number 1846 is plotting > > > > > > > > > But when i use the same command (say select water11100, residue > > > 11100) > > > > > > > > > for plotting the residue 11100 the previous command does not work > > > > > > > > > How to tackle this problem. Thanks in advance for your help > > > > > > > > > Stephane > > > > > > > > > > > > > -------------------------------------------------------------- > ---------------- > Crystal Reports - New Free Runtime and 30 Day Trial Check out > the new simplified licensing option that enables unlimited > royalty-free distribution of the report engine for externally > facing server and web deployment. > http://p.sf.net/sfu/businessobjects > _______________________________________________ > 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 > > > > > ------------------------------------------------------------------------------ Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ 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
