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superseded by merged pdbml. So basically j'm just a bit outdated and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 agai
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 nu
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
wa
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! Simp
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 overnig
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 i
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.
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
-
Hello List,
is there any good reason why PyMOL can not read PDBML data files ?
Cheers,
Jerome
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