Re: [PyMOL] default fetch format
You may want to form you own opinion and take a look at this thread and others
in CCP4
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;8e513bea.1308
I hope the link works. There has been extensive and heated debate over the
merits of mmCIF vs. PDB on the same BB. The wwPDB is pushing mmCIF, which was
developed as an ARCHIVAL format, but in my opinion the community as a whole is
rather reluctant to accept mmCIF as a WORKING format. The distinction between a
working and archiving format is vital in this context.
As far as I am concerned the PDB format as a working format is unmatched in its
utility (try to concatenate 2 structures in both formats or prepare a file for
MR and you see what I mean), but has drawbacks, some of which would be adapted
by an extended PDB format.
So as long as the current programs support PDB, I really could care less what
the wwPDB thinks; however if programs drop support for the PDB format, I'll be
more than happy to look for alternatives...
Cheers,
Carsten
-Original Message-
From: Albert [mailto:mailmd2...@gmail.com]
Sent: Sunday, November 22, 2015 2:23 PM
To: Thomas Holder
Cc: pymol-users
Subject: Re: [PyMOL] default fetch format
Hi Thomas:
thanks a lot for helpful advice.
May I ask is there any superior features of mmCIF format against PDB format?
regards
Albert
On 11/22/2015 04:15 PM, Thomas Holder wrote:
> Hi Albert,
>
> Unfortunately the default fetch type can't be configured. But you can
> override the fetch command. Example which you could place in your ~/.pymolrc
> file:
>
> python
> from pymol import cmd
>
> def fetchpdb(*args, **kwargs):
> if 'type' not in kwargs:
> kwargs['type'] = 'pdb'
> return cmd.fetch(*args, **kwargs)
>
> cmd.extend('fetch', fetchpdb)
> python end
>
> However, if you don't have a compelling reason to work with PDB instead of
> mmCIF, then I recommend to give the new mmCIF default a try.
>
> Cheers,
--
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Re: [PyMOL] default fetch format
Hi Albert,
Unfortunately the default fetch type can't be configured. But you can override
the fetch command. Example which you could place in your ~/.pymolrc file:
python
from pymol import cmd
def fetchpdb(*args, **kwargs):
if 'type' not in kwargs:
kwargs['type'] = 'pdb'
return cmd.fetch(*args, **kwargs)
cmd.extend('fetch', fetchpdb)
python end
However, if you don't have a compelling reason to work with PDB instead of
mmCIF, then I recommend to give the new mmCIF default a try.
Cheers,
Thomas
On 19 Nov 2015, at 13:47, Albert wrote:
> Hello:
>
> I noticed that if we run command:
>
> fetch 2ac1
>
> to get PDB into pymol in Version 1.8.0, it downloaded .cif file by
> default. I am just wondering is it possible to change the default format
> as .pdb file?
>
> thanks a lot
>
> Albert
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
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Re: [PyMOL] default fetch format
Hi Albert, > May I ask is there any superior features of mmCIF format against PDB format? It solves all the identifier limitations of the PDB format, like number of chains, number of residues, and number of atoms. Besides that, the PDB format will be phased out by the wwPDB in favor of the mmCIF format, which is the new standard since 2014. See also http://mmcif.wwpdb.org/docs/faqs/pdbx-mmcif-faq-general.html Cheers, Thomas -- 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] default fetch format
Hi Thomas:
thanks a lot for helpful advice.
May I ask is there any superior features of mmCIF format against PDB format?
regards
Albert
On 11/22/2015 04:15 PM, Thomas Holder wrote:
> Hi Albert,
>
> Unfortunately the default fetch type can't be configured. But you can
> override the fetch command. Example which you could place in your ~/.pymolrc
> file:
>
> python
> from pymol import cmd
>
> def fetchpdb(*args, **kwargs):
> if 'type' not in kwargs:
> kwargs['type'] = 'pdb'
> return cmd.fetch(*args, **kwargs)
>
> cmd.extend('fetch', fetchpdb)
> python end
>
> However, if you don't have a compelling reason to work with PDB instead of
> mmCIF, then I recommend to give the new mmCIF default a try.
>
> Cheers,
--
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[PyMOL] default fetch format
Hello: I noticed that if we run command: fetch 2ac1 to get PDB into pymol in Version 1.8.0, it downloaded .cif file by default. I am just wondering is it possible to change the default format as .pdb file? thanks a lot Albert -- ___ 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
