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Today's Topics:
1. Re: combine distance objects (Robert Campbell)
2. [Re: [PyMOL] combine distance objects] (Viktor Hornak)
3. Re: combine distance objects (Michael George Lerner)
4. RE: combine distance objects (Garcia, Tzintzuni I.)
--__--__--
Message: 1
Date: Tue, 8 Mar 2005 10:55:20 -0500
From: Robert Campbell <r...@post.queensu.ca>
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] combine distance objects
Hi,
Daniel Farrell [Monday, March 07, 2005 1:23 PM] wrote:
I want to create a lot of distance objects (in the hundreds)
between particular atomic pairs. Obviously I can make a
script like the following, inserting the exact atomic
selections that I want:
distance distobj12 = (atom1), (atom2)
distance distobj34 = (atom3), (atom4)
... etc.
However, I will end up with hundreds of distance object
controls on the right side of the pymol viewer. I want to
have just a SINGLE distance object that contains all of the
individual distance objects combined.
That way I could enable/disable the entire object with a
single click, or change the color, etc. Hundreds of
individual objects would be unmanageable.
Is there a way to do this? Thanks,
* Warren L. DeLano <war...@delanoscientific.com> [2005-03-07 13:46]
wrote:
This is a reasonable request, but no, it isn't possible right now --
sorry.
If it isn't necessary to be able to turn the distances on and off,
then you
can name them using a preceeding underscore "_" so that they are
omitted
from the object list.
But in fact one *can* still turn them on and off, with the "enable" or
"disable" command on the command line:
enable _dist1
disable _dist1
And it would be straightforward to put those commands within a loop:
# turn them all off:
for i in range(100):
cmd.disable("_dist1%s" % i)
# turn them all on:
for i in range(100):
cmd.enable("_dist1%s" % i)
Change "100" to whatever is appropriate.
Cheers,
Rob
--
Robert L. Campbell, Ph.D.
<r...@post.queensu.ca>
Senior Research Associate phone:
613-533-6821
Dept. of Biochemistry, Queen's University, fax:
613-533-2497
Kingston, ON K7L 3N6 Canada
http://adelie.biochem.queensu.ca/~rlc
PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
--__--__--
Message: 2
Date: Tue, 08 Mar 2005 11:31:16 -0500
From: Viktor Hornak <hor...@csb.sunysb.edu>
To: pymol-users@lists.sourceforge.net
Subject: [Re: [PyMOL] combine distance objects]
Robert Campbell wrote:
Hi,
Daniel Farrell [Monday, March 07, 2005 1:23 PM] wrote:
I want to create a lot of distance objects (in the hundreds)
between particular atomic pairs. Obviously I can make a
script like the following, inserting the exact atomic
selections that I want:
distance distobj12 = (atom1), (atom2)
distance distobj34 = (atom3), (atom4)
... etc.
However, I will end up with hundreds of distance object
controls on the right side of the pymol viewer. I want to
have just a SINGLE distance object that contains all of the
individual distance objects combined.
That way I could enable/disable the entire object with a
single click, or change the color, etc. Hundreds of
individual objects would be unmanageable.
Is there a way to do this? Thanks,
* Warren L. DeLano <war...@delanoscientific.com> [2005-03-07 13:46]
wrote:
This is a reasonable request, but no, it isn't possible right now --
sorry.
If it isn't necessary to be able to turn the distances on and off,
then you
can name them using a preceeding underscore "_" so that they are
omitted
from the object list.
But in fact one *can* still turn them on and off, with the "enable" or
"disable" command on the command line:
enable _dist1
disable _dist1
And it would be straightforward to put those commands within a loop:
# turn them all off:
for i in range(100):
cmd.disable("_dist1%s" % i)
# turn them all on:
for i in range(100):
cmd.enable("_dist1%s" % i)
Change "100" to whatever is appropriate.
Cheers,
Rob
Even though the scripting of this sort is flexible and will get you
what
you want, I'd still support Daniels's suggestion. Grouping multiple
objects (not just distances) would be extremely useful because one can
split the objects into functional or logical units and collectively
manipulate their properties (e.g. color, state, graphical
representation) and it would be more interactive than scripting the
same
functionality. I can imagine however, that incorporating object
hierarchy/grouping into PyMol may not be a trivial task...
Cheers,
-Viktor
--
=============================
Viktor Hornak
Center for Structural Biology
SUNY at Stony Brook
=============================
--__--__--
Message: 3
Date: Tue, 8 Mar 2005 11:42:28 -0500 (EST)
From: Michael George Lerner <mler...@umich.edu>
To: Robert Campbell <r...@post.queensu.ca>
cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] combine distance objects
On Tue, 8 Mar 2005, Robert Campbell wrote:
Hi,
Daniel Farrell [Monday, March 07, 2005 1:23 PM] wrote:
I want to create a lot of distance objects (in the hundreds)
between particular atomic pairs. Obviously I can make a
script like the following, inserting the exact atomic
selections that I want:
distance distobj12 = (atom1), (atom2)
distance distobj34 = (atom3), (atom4)
... etc.
But in fact one *can* still turn them on and off, with the "enable" or
"disable" command on the command line:
enable _dist1
disable _dist1
And it would be straightforward to put those commands within a loop:
# turn them all off:
for i in range(100):
cmd.disable("_dist1%s" % i)
# turn them all on:
for i in range(100):
cmd.enable("_dist1%s" % i)
Change "100" to whatever is appropriate.
I was just about to write something like this. In fact, I have tons of
files called something like x.py sprinkled around that do things like
-----------------------------------------
from pymol import cmd
num_dist = 100
def show_dist():
""" show all of my distance objects """
for i in range(num_dist):
cmd.enable('_dist%s'%i)
def hide_dist():
""" hide all of my distance objects """
for i in range(num_dist):
cmd.disable('_dist%s'%i)
cmd.extend('sd',show_dist)
cmd.extend('hd',hide_dist)
-----------------------------------------
You could also try something cute like
def show_dist():
dists = [name for name in cmd.get_names() if cmd.get_type(name) ==
'object:distance']
for name in dists: cmd.enable(name)
etc.
if you don't want to have to keep track of how many there are.
-michael
--
www.umich.edu/~mlerner | _ |Michael Lerner
This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan
it's a cheer-ocracy. | - against HTML email X | Biophysics
-Torrence, Bring It On| / \ | mler...@umich
Cheers,
Rob
--
Robert L. Campbell, Ph.D.
<r...@post.queensu.ca>
Senior Research Associate phone:
613-533-6821
Dept. of Biochemistry, Queen's University, fax:
613-533-2497
Kingston, ON K7L 3N6 Canada
http://adelie.biochem.queensu.ca/~rlc
PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
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--__--__--
Message: 4
Subject: RE: [PyMOL] combine distance objects
Date: Tue, 8 Mar 2005 14:11:39 -0600
From: "Garcia, Tzintzuni I." <tzgar...@utmb.edu>
To: <pymol-users@lists.sourceforge.net>
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