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Today's Topics:
1. RE: plane2colour (Warren L. DeLano)
2. RE: mpng command (Warren L. DeLano)
3. RE: plane2colour (Warren L. DeLano)
4. Changing lines to be dashed lines (Michael Tallhamer)
5. stereo on rh9 ? (Cameron Mura)
6. (no subject) (mkienetz)
7. Re: (no subject) (Cameron Mura)
8. RE: Changing lines to be dashed lines (Warren L. DeLano)
9. CGOs and TRIANGLE primitive (Mike Brown)
10. 2 questions about Summit drivers w/ Radeon8500 card for stereo... (Cameron
Mura)
11. Labels (roidis alexandros)
12. Re: Labels (Scott Classen)
13. RE: Labels (Warren L. DeLano)
--__--__--
Message: 1
From: "Warren L. DeLano" <war...@delanoscientific.com>
To: "'Warren L. DeLano'" <war...@delanoscientific.com>,
=?iso-8859-1?Q?'Bj=F6rn_Kauppi'?= <bjorn.kau...@karobio.se>,
<pymol-users@lists.sourceforge.net>
Subject: RE: [PyMOL] plane2colour
Date: Tue, 27 May 2003 14:16:58 -0700
Whoops, clarification. I misinterpreted the question...
ray_interior_color meets a different need. So far, there isn't any
plane2color-like feature in PyMOL. Sorry for the confusion.
Cheers,
Warren
-----Original Message-----
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Warren L.
DeLano
Sent: Tuesday, May 27, 2003 9:19 AM
To: 'Bj=F6rn Kauppi'; pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] plane2colour
Bjorn,
Good news, I just recently added opaque, colored, "insides" of cartoons,
surfaces, and spheres to the upcoming release. =20
In version 0.88 and beyond, "set interior_color, color-name" will
achieve this effect.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154=20
Fax (650)-593-4020
-----Original Message-----
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Bj=F6rn
Kauppi
Sent: Tuesday, May 27, 2003 6:49 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] plane2colour
Hi,
Is it an equivalent in PyMOL to the plane2colour command in Molscript?
i.e. controlling the colour of the "inside" of an cartoon-drawn helix?
Or can I get a similar effect with PyMOL somehow?
Bj=F6rn
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--__--__--
Message: 2
From: "Warren L. DeLano" <war...@delanoscientific.com>
To: "'Jason Thomas Maynes'" <ja...@biochem.ualberta.ca>,
<pymol-users@lists.sourceforge.net>
Subject: RE: [PyMOL] mpng command
Date: Tue, 27 May 2003 14:24:57 -0700
Jason,
The "mpng" command in recent versions of PyMOL takes two
arguments, first and last, which control which frames are rendered. You
can have your script set these appropriately based on where the job is
running.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
-----Original Message-----
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Jason
Thomas Maynes
Sent: Tuesday, May 27, 2003 9:57 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] mpng command
Hello:
Does anybody know if you can specify certain movie frames to render and
write out (ie. to batch render movie frames on different computers)
other
than just dicing up one movie into four or five different scripts and
piecing them together.
Thanks in advance.
Cheers,
JTM
"We can be sure that if a detailed understanding of the molecular basis
of
chemo-therapeutic activity were to be obtained, the advance of medicine
would be greatly accelerated."
Linus Pauling, Nobel Laureate 1954
"...everything that living things do can be understood in terms of the
jigglings and wigglings of atoms."
Richard Feynman
*************************
Jason Thomas Maynes
PhD/MD Program
Department of Biochemistry
Faculty of Medicine
University of Alberta
ja...@biochem.ualberta.ca
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--__--__--
Message: 3
From: "Warren L. DeLano" <war...@delanoscientific.com>
To: =?iso-8859-1?Q?'Bj=F6rn_Kauppi'?= <bjorn.kau...@karobio.se>,
<pymol-users@lists.sourceforge.net>
Subject: RE: [PyMOL] plane2colour
Date: Tue, 27 May 2003 18:37:11 -0700
PyMOLer's,=20
Okay, with apologies to Per Kraulis, I have implemented Bjorn's request.
There is now a "plane2color"-like feature in PyMOL.=20
For example figures, see http://pymol.sf.net/ms1.jpg and
http://pymol.sf.net/ms2.jpg which were both just created using PyMOL
alone, without any reliance on Molscript, though I wouldn=92t have
believed it myself if you showed them to me this morning!
The new command is:
set cartoon_highlight_color, color-name
as in=20
set cartoon_highlight_color, grey70
If you can compile PyMOL source code from the CVS repository, then you
can access this feature right away. Otherwise, look for it in the
upcoming 0.88 release.
Sorry for all the extra traffic on this thread today, but it isn't often
that we get a new feature request from a major PyMOL sponsor that can
actually be met that same day.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154=20
Fax (650)-593-4020
-----Original Message-----
From: Warren L. DeLano [mailto:war...@delanoscientific.com]=20
Sent: Tuesday, May 27, 2003 1:17 PM
To: 'Warren L. DeLano'; 'Bj=F6rn Kauppi';
'pymol-users@lists.sourceforge.net'
Subject: RE: [PyMOL] plane2colour
Whoops, clarification. I misinterpreted the question...
ray_interior_color meets a different need. So far, there isn't any
plane2color-like feature in PyMOL. Sorry for the confusion.
Cheers,
Warren
-----Original Message-----
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Warren L.
DeLano
Sent: Tuesday, May 27, 2003 9:19 AM
To: 'Bj=F6rn Kauppi'; pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] plane2colour
Bjorn,
Good news, I just recently added opaque, colored, "insides" of cartoons,
surfaces, and spheres to the upcoming release. =20
In version 0.88 and beyond, "set interior_color, color-name" will
achieve this effect.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154=20
Fax (650)-593-4020
-----Original Message-----
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Bj=F6rn
Kauppi
Sent: Tuesday, May 27, 2003 6:49 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] plane2colour
Hi,
Is it an equivalent in PyMOL to the plane2colour command in Molscript?
i.e. controlling the colour of the "inside" of an cartoon-drawn helix?
Or can I get a similar effect with PyMOL somehow?
Bj=F6rn
--__--__--
Message: 4
From: "Michael Tallhamer" <tallha...@hotmail.com>
To: pymol-users@lists.sourceforge.net
Date: Wed, 28 May 2003 14:32:21 -0400
Subject: [PyMOL] Changing lines to be dashed lines
PyMOLers
Is it possible to change the lines that represent bonds to dashed lines like
the ones used for distaces so I can change the radius and width parameters.
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--__--__--
Message: 5
Date: Wed, 28 May 2003 12:38:04 -0700
From: Cameron Mura <cm...@mccammon.ucsd.edu>
Reply-To: cm...@mccammon.ucsd.edu
Organization: UCSD
To: pymol-users@lists.sourceforge.net, o-i...@origo.imsb.au.dk
Subject: [PyMOL] stereo on rh9 ?
[sorry to send this to both lists, but I think it may be applicable...]
Dear O & PyMOLers,
Have any of you experienced difficulty with stereo on RedHat 9??
With PyMOL, trying to switch to stereo view results in the "Error:
Selected stereo mode is not available.", and in O the error is this:
"GLUT: Fatal Error in lin_ono_9.0.0: visual with necessary capabilities
not found." I suspect the root of both problems is the same.
I checked the shared library dependencies of O (which seem okay from the
output of "ldd /path-to-o/lin_ono*"), and verified that the glut-3.7-13
package was installed (rpm -q glut-3.7-13), as well as the following
two Mesa-related packages:
XFree86-Mesa-libGLU-4.3.0-2
XFree86-Mesa-libGL-4.3.0-2
Stereo mode for both of these programs worked fine in a previous
installation in which I was running red hat 8. With the current systems,
I did a fresh install of rh9 (shrike) on two machines:
(1) a Dell XEON machine with an NVidia Quadro4 700 XGL graphics card,
using the NVIDIA Kernel Module 1.0-4363 (with a ViewSonic flatpanel
monitor -- so I don't expect to actually do true Quad-buffered stereo
displays or anything like that, mainly just testing)
(2) a PC with a ViewSonic P225f CRT monitor (this is the system I would
actually like to use for stereo), powered by an ATI Radeon 8500LE
graphics card.
If anyone has encountered similar difficulties or has any helpful hints,
I'd greatly appreciate hearin bout it!
Cameron
