Dear Pymol Users,
I've found a problem with Pymol version 1.4.1. I am using Ubuntu 10.10 in a
laptop with Intel Mobile 4 graphics controller.
The problem comes when I load any PDB file, then try to show it as a
cartoon. It displays the cartoon but in black color, so I cannot see it
unless I turn
Hello Santiago,
have you tried using the graphics drivers from the xorg-edgers project?
That helped me with the stick coloring problem:
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg09210.html
and may also help with your problem.
Bernhard
-Original Message-
From:
Hi Bernhard,
I just installed this new driver :
xserver-xorg-video-intel_2.13.901-2ubuntu2~xup~maverick_i386.deb
And the problem remains the same. Also tried installing the combo of :
libdrm-intel1_2.4.23+git20110119.550fe2ca-0ubuntu0sarvatt~maverick_i386.deb
Hi Santiago,
I've found a problem with Pymol version 1.4.1. I am using Ubuntu 10.10 in a
laptop with Intel Mobile 4 graphics controller.
The problem comes when I load any PDB file, then try to show it as a
cartoon. It displays the cartoon but in black color, so I cannot see it
unless I turn
Dear community,
I was searching the internet for several days now to find out how to perform a
distance dependent coloring in pymol.
The idea is to color the surface of a viral (spherical) structure. I would like
to define the xyz-coordinates of the center of the viral structure an color all
Hi Jason,
Thanks for your prompt reply.
2011/7/28 Jason Vertrees jason.vertr...@schrodinger.com
This only happens if I use the set use_shaders, 1. If I don't use this
command, the cartoon and stick are displayed in the right colour, but
then I have problems coloring the sticks (it's a
Hi Robert,
you can set the distance between each atom and the center as b-factor,
and then use spectrum (or spectrumany [1]) for coloring.
I wrote a small python script that will do that, see attachment.
Example (in PyMOL command line):
run distancecoloring.py
centerdistance2b (all)
Hi Robert,
I did something like this in the past. Check out the ramp_new command
page on the PyMOLWiki for an example
(http://pymolwiki.org/index.php/Ramp_new#Elaborate_examples) for
arbitrary functions.
Here's a very quick way to color a surface by distance from a given
point--here I chose the
I have a slightly different answer using (almost:) only PyMOL commands:
# take 1acb as example
fetch 1acb, async=0
import numpy
# center is [x0,y0,z0]
x0,y0,z0=[1,2,3]
alldist = []
iterate_state 1, 1acb,
alldist.append(numpy.sqrt(numpy.sum([(x-x0)**2,(y-y0)**2,(z-z0)**2])))
# assign dist to
