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 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ _______________________________________________ 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
