Hi Thomas, thank you very much for help.
Since PDB made pdbml default for large systems (i'm particularly interested in ribosomes) it was a kind of pain. And it seems i have to upgrade my PyMOL and read documentation more often: help for fetch in PyMOL from svn shows '{default: cif (default was "pdb" up to 1.7.6)}'. Regards, Arthur On 23.10.2015 00:48, Thomas Holder wrote: > Hi Arthur, > > The script I sent you earlier had one Incentive PyMOL specific line > and won't work in Open-Source PyMOL unless you delete that line. My > apologies. > > However, if you are compiling the latest code from SVN you don't need > the script, I already have incorporated it into the code base! Simply > load files with .xml or .pdbml extension. > > I have to add that loading 4v50 in PDBML format into PyMOL is a rather > bad idea. PDBML is utterly bloated, the uncompressed file for 4v50 is > over 300MB, and the in-memory xml representation will explode into the > gigabytes. You should really use mmCIF format instead, PyMOL loads > 4v50.cif in 2 seconds. > > Cheers, > Thomas > > On 22 Oct 2015, at 12:38, Arthur Zalevsky <aozalev...@fbb.msu.ru> > wrote: > >> Hi Thomas! >> >> I've tried your parser with pymol 1.4.1 from ubuntu 12.04 repos and >> freshly compiled 1.7.7.2 from svn with no luck at all. I've tried to >> load PDB ID 4V50 (full E.coli ribosome). Pymol simply hangs with 100% >> cpu usage. >> >> From 1.4.1 i've got following traceback (after i left it overnight): >> >> Traceback (most recent call last): >> File "/usr/lib/python2.7/dist-packages/pymol/parser.py", line 254, >> in >> parse >> self.result=apply(layer.kw[0],layer.args,layer.kw_args) >> File "/home/domain/silwer/Downloads/load_pdbml.py", line 80, in >> load_pdbml >> atom.properties['entity_id'] = child.text or '' >> File "/usr/lib/python2.7/dist-packages/chempy/__init__.py", line 59, >> in __getattr__ >> raise AttributeError(attr) >> AttributeError: properties >> >> Any help would be appreciated. >> >> >> Regards, >> Arthur >> >> >> On 25.09.2015 01:50, Thomas Holder wrote: >>> Hi Arthur & Jerome, >>> >>> I wrote a basic PDBML importer for PyMOL, see attached script which >>> adds a "load_pdbml" command. I meant to assess the complexity of such >>> a project and ended up writing the entire thing. So far, this only >>> reads atoms and symmetry information. If you find this useful we can >>> include that in the next PyMOL release. >>> >>> Cheers, >>> Thomas >>> >>> >>> >>> On 23 Sep 2015, at 03:27, Arthur Zalevsky <aozalev...@fbb.msu.ru> >>> wrote: >>> >>>> Sorry for bumping old thread, but is support for pdbml still >>>> unimplemented? In such case i think it's a good project for our >>>> students. >>>> >>>> Regards, >>>> Arthur >>>> >>>>> From: Thomas Holder <speleo3@us...> - 2013-12-02 19:23:18 >>>>> Hi Jerome, >>>>> >>>>> I think the simple reason is that nobody ever wrote a PDBML parser >>>>> for >>>>> PyMOL. Is that a good reason? >>>>> >>>>> Cheers, >>>>> Thomas >>>>> >>>>>> On 28 Nov 2013, at 13:21, Jerome BENOIT <g6299304p@...> wrote: >>>>>> Hello List, >>>>>> >>>>>> is there any good reason why PyMOL can not read PDBML data files ? >>>>>> >>>>>> Cheers, >>>>>> Jerome ------------------------------------------------------------------------------ _______________________________________________ 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