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 <[email protected]>
> 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 <[email protected]>
>>> 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
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