Hi John, Yeah, i know about limitations of PDB format. I've missed the news you mentioned so it was a kind of surprise when i found ribosome pdbs superseded by merged pdbml. So basically j'm just a bit outdated and updating of once established pipelines is always a bit frustrating.
Thanks again, Thomas and John. Regards, Arthur On 23.10.2015 10:17, John Berrisford wrote: > Dear Authur > > As the PDB format is not suitable for structures with over 99,999 atom > lines > or over 62 chains we only distribute these structures in both mmCIF and > PDBML > formats. > > See: > http://www.wwpdb.org/news/news?year=2014#10-December-2014 > > > We (PDBe) have been using mmCIF format in pymol for number of years to > generate our images. > See: > pdbe.org/4v50 > > Regards > > John > PDBe depositions > > > On Friday 23 October 2015 07:21:07 Arthur Zalevsky wrote: >> 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 >> ------------------------------------------------------------------------------ _______________________________________________ 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
