Re: [PyMOL] pdbml
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
> 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
>>> 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 - 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 wrote:
>> Hello List,
>>
>> is there any good reason why PyMOL can not read PDBML data files ?
>>
>> Cheers,
>> Jerome
--
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Re: [PyMOL] pdbml
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 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 >> 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 - 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 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
Re: [PyMOL] pdbml
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 > 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 - 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 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
