These settings affect the atomistic representations upon
instantiation. So, keeping it simple and very fast is best. I might
add a few more settings along these lines, but I don't think I'm going
to make it totally generic.
Here's another reason why I love PyMOL: 5 minutes of coding gets you
a personalized solution to this problem. Just change "cartoon" to
whatever representation you want, or add other intermediate commands.
Here's the code:
# visLoad -- simple load wrapper that enables your desired visualization
#
# save this to a file called "visLoad.py" and then run that file
# "run /path/to/visLoad.py". visLoad will now be defined for
# you in PyMOL.
#
import string
import os
from os import path
def visLoad(filename, object=None, *args, **kwargs):
if object==None:
object = string.split(os.path.basename(filename),".")[0]
cmd.set("suspend_updates")
try:
cmd.load(filename, object, *args, **kwargs)
cmd.show_as("cartoon", object)
finally:
cmd.set("suspend_updates", "off")
cmd.extend("visLoad", visLoad)
Cheers,
-- Jason
On Tue, Mar 16, 2010 at 1:16 AM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:
> Hi Jason,
>
> Along those lines, would it be possible to have a 'default' which can
> be set to a list of settings related to appearance? That might be more
> concise than to have everything in a separate setting.
>
> set default,[cartoon, lines, nonbonded, cbaw]
>
> The default value as pymol starts up now would be [lines, nonbonded, cbag].
>
> Just my 2 eurocents...
>
> Cheers,
>
> Tsjerk
>
>
> On Tue, Mar 16, 2010 at 12:53 AM, Jason Vertrees
> <jason.vertr...@schrodinger.com> wrote:
>> David,
>>
>> You may remember writing:
>>
>>> A Pymol Quicklook plugin. My primary purpose would be for pses, but you
>>> might as well pick up pdbs and other formats supported by pymol along the
>>> way.
>>> For pdb files, I wouldn't want the default pymol view of lines colored by
>>> atom with green carbons being what I quicklook to, so either reading
>>> .pymolrc to get a default view or some variant ( .pymolqlrc ?) would be
>>> nice to allow users to customize their views. Also, maybe default to a
>>> cartoon representation colored by chains with het atoms as sticks and
>>> metals as spheres, but that's probably just forcing the view I want on
>>> others when I could just stick that in my personal .pymolqlrc type file.
>>
>> Well, reading through the source today, I found a couple settings that
>> few know about--and I might add more similar settings:
>>
>> auto_show_lines == show a newly loaded object with lines representation?
>> auto_show_spheres == show a newly loaded object with spheres representation?
>> auto_show_nonbonded == show newly loaded non-bonded?
>>
>> If these are considered useful, I can add others like:
>>
>> auto_show_cartoon(s)
>>
>> # example
>> set auto_show_spheres
>> fetch 1cll
>>
>> This offers some more flexibility for the user to choose lines or
>> other default representation.
>>
>> Cheers,
>>
>> -- Jason
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrodinger, LLC
>>
>> (e) jason.vertr...@schrodinger.com
>> (o) +1 (603) 374-7120
>>
>> ------------------------------------------------------------------------------
>> Download Intel® Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
>> proactively, and fine-tune applications for parallel performance.
>> See why Intel Parallel Studio got high marks during beta.
>> http://p.sf.net/sfu/intel-sw-dev
>> _______________________________________________
>> 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
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
>
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
------------------------------------------------------------------------------
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
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