date:20151023

[PyMOL] CGO segmentation fault

2015-10-23 Thread Tsjerk Wassenaar

Hi Thomas,

Not sure if I ever reported this already, but when cmd.load_cgo gets an
argument that is not a list of values, Pymol (1.7.4.0 incentive, Mac) halts
with a segmentation fault. I know it's my bad for feeding a still nested
list, but a segmentation fault is a harsh way of complaining :)

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.
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Re: [PyMOL] CGO segmentation fault

2015-10-23 Thread Thomas Holder

Hi Tsjerk,

Thanks for reporting, we'll look into that.

Cheers,
  Thomas

On 23 Oct 2015, at 05:14, Tsjerk Wassenaar  wrote:

> Hi Thomas,
> 
> Not sure if I ever reported this already, but when cmd.load_cgo gets an 
> argument that is not a list of values, Pymol (1.7.4.0 incentive, Mac) halts 
> with a segmentation fault. I know it's my bad for feeding a still nested 
> list, but a segmentation fault is a harsh way of complaining :)
> 
> Cheers,
> 
> Tsjerk
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] pdbml

2015-10-23 Thread Arthur Zalevsky

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

2015-10-23 Thread Arthur Zalevsky

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 
>> >
>> > 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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>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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>> 

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[PyMOL] CGO segmentation fault

Re: [PyMOL] CGO segmentation fault

Re: [PyMOL] pdbml

Re: [PyMOL] pdbml

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