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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