On 15:47 Thu 10 Nov , Jason Vertrees wrote:
> As has always been the case, some new features added to Incentive
> PyMOL v1.5.0 will not be immediately added to the open-source project,
> as Incentive subscribers pay to have priority access to these new
> features.
I always wonder, are there
On 21:37 Thu 28 Apr , lina wrote:
> Error: 1
> Exception in Tk callback
> Function: > (type: 'instancemethod'>)
> Args: ()
> Traceback (innermost last):
> File "/usr/lib/python2.6/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py",
> line 1747, in __call__
> return apply(self.func, args)
>
On 17:39 Tue 12 Oct , Cristina RodrÃguez wrote:
> All it's alright! It gives me the right outputs, but when I want to
> visualize them in the "View Pose" window, I can't load anything! I've
> tried with *.pdbqt and *.dlg files obtained from Autock/Vina and
> Autodock4 respectively. Is it po
On 13:38 Fri 20 Nov , Stephen P. Molnar wrote:
> I had successfully compiled Plymol from the Subversion repository in
> OpenSuSE v103. Linux.
>
> I say successfully, because I have just upgraded my linux computer to
> OpenSuSE v11.2. Unfortunaltely, I have a bit of a problem compiling the
> s
Hi all,
I'm trying to get the light sources to look a certain way for a
raytraced image. When I go into the settings via "Edit All" and search
for "light", I see 9 light sources. I tried to rearrange the ordering by
just copying and pasting them around then hitting return, but it didn't
seem t
tion scores into the
B-factor field using ConSurf, then comparing two homologs to look at
gain-of-function and loss-of-function overlaid as color on a single
structure. Bright red or blue indicate the most interesting differences.
--
Thanks,
Donnie
Donnie Berkholz
P. Andrew Karplus lab
Oregon S
On 10:11 Sun 12 Jul , Jason Vertrees wrote:
> Donnie Berkholz wrote:
> > I'm trying to compare the B-factors in two homologous proteins I
> > aligned using 'super'. I can create an alignment object mapping
> > residue pairs together, so I think what I wan
two CA B's onto one
of the structures, then color it by B-factor and color unaligned
residues gray.
I can't even figure out how to get at the alignment object or what's in
it, much less how to do this. Could anyone help me?
--
Thanks,
Donnie
Donnie Berkholz
P. Andrew
On 21:38 Thu 09 Jul , Donnie Berkholz wrote:
> On 17:24 Tue 30 Jun , Buz Barstow wrote:
> > I have a very large library (almost 1000) of similar genetic
> > sequences, for which I would like to generate homology models. Does
> > anyone know of a way to automate r
gh pymol, or alternatively through
> python?
There's a framework called Biskit that you can use to do it all locally.
--
Thanks,
Donnie
Donnie Berkholz
P. Andrew Karplus lab
Oregon State University
--
Enter the
archive/forum.php?forum_name=pymol-users>
--
Thanks,
Donnie
Donnie Berkholz
P. Andrew Karplus lab
Oregon State University
pgpvigVU2y0b8.pgp
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--
Register Now for Creativity and Technology (CaT), Ju
se all of the parts of them in some sort of
Frankenstein setup pending support for LCD stereo.
--
Thanks,
Donnie
Donnie Berkholz
Developer, Gentoo Linux
Blog: http://dberkholz.wordpress.com
pgpn9D1b93hj3.pgp
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DB with a conservation index
in the B-factor field. You can then load that into PyMol and color by B
as usual.
Since it's unclear exactly what you intend to do with this, I can't tell
you whether ConSurf makes sense for your use.
--
Thanks,
Donnie
Donnie Berkholz
Developer, Gent
rce I found of
that report:
"Quad Buffered Stereo will be supported with the NVIDIA GeForce 3D
vision glasses in upcoming driver release by spring 2009."
<http://www.nvidia.com/object/quadro_stereo_technology.html>
--
Thanks,
Donnie
Donnie Berkholz
Developer, Gentoo Li
On 11:28 Sat 12 Jan , DeLano Scientific wrote:
> > Output:
> > 'ObjectMolecule: Read crystal symmetry information.
> > Symmetry-Error: Urecognized space group symbol 'C 1 2 1'.
> > Symmetry-Error: Unable to get matrices from sglite.
> > CmdLoad: "pdb/1f5n.pdb" loaded as "1f5n".'
> >
> > I'm us
DeLano Scientific wrote:
> I believe Donnie is mistaken: PyMOL runs just fine with FreeGLUT 2.4.0
> (don't know about all 2.4.x though). Lack of an ability to create a direct
> rendering context is most likely a problem with your graphics driver, X11
> configuration, pixel depth, or with the inte
Hugo Gutiérrez de Teran wrote:
> freeglut (/home/hteran/tmp/programs/pymol/pymol.exe): Unable to create
> direct context rendering for window 'PyMOL Viewer' This may hurt
> performance.
>
> But my system says I have freeglut installed:
>
> # yum search glut
> freeglut.i386
DeLano Scientific wrote:
> Donnie,
>
> Hmm...it seems "ObjectGroup.c" was left out of setup.py. It should be fixed
> now.
>
> Thanks for the reminder!
Thanks much! I really appreciate your quick response.
Thanks again,
Donnie
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I've been unable to start PyMOL from recent subversion builds. It worked
in r2738 but fails in 2740 and newer (possibly 2739 as well, didn't
check). Here's what I get:
Traceback (most recent call last):
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 109, in ?
import pymol
Younes wrote:
> (1) I have tried following Warren's procedure to position labels in space:
>
> http://www.dl.ac.uk/list-archive-public/ccp4bb/2006-01/msg00695.html
>
> The following step did not seem to work:
>
> "then ctrl-middle-click-and-drag to position the label in space"
>
> I am using Py
DeLano Scientific wrote:
> PyMOL Users,
>
> We have gotten a couple of questions recently regarding running nVidia-based
> Stereo 3D under the "X.org" X-server instead of using XFree86.
>
> We don't have X.org set up in house yet, so I was hoping someone else might
> be able to provide a defini
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