Looking at the code around fetch, it seems pymol makes an assumption that has annoyed me in many other pieces of software, that there is only one biological assembly in the pdb. Lots of proteins have 2 or more. I think I've even seen one with 6.
The second biological assembly has an extension of pdb2, the third has an extension of pdb3, etc. For an example, see 2pab, which has two different biological assemblies. As far as I can tell, pymol hardcodes only being able to get pdb1 right now. -David On Thu, Aug 5, 2010 at 5:47 PM, Jason Vertrees <[email protected]> wrote: > Greetings, > > Fetch has been fixed and the code checked into SVN with some other > changes. I'm calling this v1.3r1 because 'fetch' is so integral to > PyMOL. > > For Incentive PyMOL subscribers, the new v1.3r1 builds will be > available before the weekend. > > As usual please report any problems. > > Cheers, > > -- Jason > > On Wed, Aug 4, 2010 at 12:33 AM, Jason Vertrees > <[email protected]> wrote: >> Hi Daphna, >> >> The PDB servers underwent some reorganization and moved the files on >> us! I will post a fix for this by tomorrow night. >> >> Thanks! >> >> -- Jason >> >> On Sun, Aug 1, 2010 at 3:44 AM, Daphna Meroz <[email protected]> wrote: >>> Dear Sir/Madam, >>> >>> I am using MacPymol version 1.2r1. For some reason, the fetch pdb command >>> does not work anymore (the error message is "unable to load pdb"). >>> Is there some way to resolve this? >>> >>> Thank you, >>> Daphna Meroz >>> ------------------------------------------------------------------------------ >>> The Palm PDK Hot Apps Program offers developers who use the >>> Plug-In Development Kit to bring their C/C++ apps to Palm for a share >>> of $1 Million in cash or HP Products. Visit us here for more details: >>> http://p.sf.net/sfu/dev2dev-palm >>> _______________________________________________ >>> PyMOL-users mailing list ([email protected]) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/[email protected] >>> >> >> >> >> -- >> Jason Vertrees, PhD >> PyMOL Product Manager >> Schrodinger, LLC >> >> (e) [email protected] >> (o) +1 (603) 374-7120 >> > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) [email protected] > (o) +1 (603) 374-7120 > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by > > Make an app they can't live without > Enter the BlackBerry Developer Challenge > http://p.sf.net/sfu/RIM-dev2dev > _______________________________________________ > PyMOL-users mailing list ([email protected]) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/[email protected] > ------------------------------------------------------------------------------ This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev _______________________________________________ PyMOL-users mailing list ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
