Warren.
I can't speak to the alignment tools, as I don't spend a lot of time in
homology model building, but I would like to second the idea of adding the
selection keywords. They would make my use of pymol that much easier.
Andy
--On Wednesday, May 19, 2004 09:32:17 -0700 Warren DeLano
I'm a big fan of choice and suggest we have multiple options:
1) only show biopolymers with standard 1-letter codes, O for water, X for
others.
2) mix known abbreviations and full 3-letter codes with visual cues.
3) full residue names (up to 4 letters allowed)
4) chains
5) segments [rarely used no
LOL...
I found a very complex solution to a simple problem :-)
yes, pymolrc (without the dot) also works :-)
Cheers,
Esben
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
To: EPF (Esben Peter Friis); pymol-users@lists.sourceforge.net
Cc: TAPO (Thomas Agersten Poulsen)
Actually, this too was anticipated ; ). On Windows:
for PyMOL commands, simply use
pymolrc
(no extention -- I suppose pymolrc.txt or pymolrc.pml would've made more
sense...)
or for Python code:
pymolrc.py
pymolrc.pym
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L.
Hi PyMOLers
Seems like it is somewhat difficult to create a .pymolrc file in Windows
(whatever version). The standard Windows explorer file browser simply doesn't
accept this as a filename.
The workaround is to call the file something else, eg. pymolrc.txt and put the
desired commands in it u
I think it would make sense to include everything (ions, waters etc.) in the
3-letter residue view. This is straightforward, as the codes can be taken
directly from the PDB file, so PyMOL does not need to recognize them. It may be
necessary to allow for 4-letter codes also?
But in the 1-letter
Just an FYI for people trying to set up projection stereo on a budget...
Version 0.96beta2 included additional changes to facilitate this, and some
specific instructions for configuring PyMOL to work in dual-screen (passive)
stereo mode can be found on the bottom of the beta-release page.
http:
Hi,
Those of you interested in APBS-based electrostatics in PyMOL via
Michael Lerner's plugins may be interested in an RPM available at
"http://mccammon.ucsd.edu/~cmura/PYMOL_examples/pymol-0.96apbs-2rh90.i386.rpm";.
It is basically a CVS snapshot of a recent version of PyMOL (v0.96beta5;
05/
Thanks for the input.
> * sequence colors could (optionally?) match atom (C-alpha)
> colors in the 3D view.
Good idea.
> * When a 3D-alignment is done, there is a sequence alignment behind.
> Having this transferred to the sequence window would be
> extremely useful.
Planned -- but this i
Dear all,
Recently I have a problem to launch external gui which should appear
by default.I want to know if there is any way to launch it
manually.
Thank you
Sincerely,
Aidong
PyMOL takes care of this, thanks again Warren!
>
> Are you using the same platform for both Grasp and Pymol? I don't think
> that big-endian maps (written by an SGI computer) can be read by a
> little-endian platform, such as a x86 based PC.
===
Yu Chen
H
Hi Warren
This is GREAT!
I was going to suggest this for the future development, but (as usual
:-) you're ahead.
Very good points:
* possible to chose between atoms/1-letter residues/3-letter residues
etc.
* The background color of the scrollbar area shows a complete overview
of the selectio
I have mad a lot of these pictures, and the solution is to create two
objects for the substrate.
object1, displayed as sticks in the desired color, and
object2 dipslayed as spheres in the desired color(s)
and then "set sphere_scale, 0.3, object2"
Example (if the file contains a residue named "N
Are you using the same platform for both Grasp and Pymol? I don't think
that big-endian maps (written by an SGI computer) can be read by a
little-endian platform, such as a x86 based PC.
- Esben
> > The problem is getting the phi map in grasp. Can somebody
> explain me how to do it?
>
> This
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