Hi David, You're right. It's fixed now. I'll check the code in later today. PyMOL understands the types better now and it even works across the wwPDB servers. The PDB id "3by0" is a good test case; it has pdb, biounits and density data.
Test out the new code with: # let's fetch from Nihon. set fetch_host, pdbj # standard fetching fetch 3by0 # now, let's fetch from the European server set fetch_host, pdbe # test out bio units fetch 3by0, bioUnit1, type=pdb1 fetch 3by0, bioUnit2, type=pdb2 # back to US server set fetch_host, pdb # grab the 3rd bio unit fetch 3by0, bioUnit3, type=pdb3 # fetch the EDS map fetch 3by0, type=fofc Be warned that by default, PyMOL names objects based on their code, not type (except for maps), and PyMOL loads objects with the same name into the same object but increments the state. You can turn this off with set auto_rename_duplicate_objects, Cheers, -- Jason On Fri, Aug 6, 2010 at 8:25 AM, David Hall <li...@cowsandmilk.net> wrote: > 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 > <jason.vertr...@schrodinger.com> 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 >> <jason.vertr...@schrodinger.com> 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 <daphname...@gmail.com> 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 (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 >>>> >>> >>> >>> >>> -- >>> Jason Vertrees, PhD >>> PyMOL Product Manager >>> Schrodinger, LLC >>> >>> (e) jason.vertr...@schrodinger.com >>> (o) +1 (603) 374-7120 >>> >> >> >> >> -- >> Jason Vertrees, PhD >> PyMOL Product Manager >> Schrodinger, LLC >> >> (e) jason.vertr...@schrodinger.com >> (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 (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 >> > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (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 (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
