RE: [PyMOL] Ray Tracing Crash

2004-01-21 Thread Warren L. DeLano
Morri, The RH9 Patch is described and published on: https://rhn.redhat.com/errata/RHBA-2003-136.html I would not expect Debian to suffer from the same crash. If it does, then we may be dealing with a genuine bug in PyMOL (assuming that you're not simply running out of RAM). With respect to De

Re: [PyMOL] Ray Tracing Crash

2004-01-21 Thread Michael Banck
On Tue, Jan 20, 2004 at 10:52:17PM -0800, Morri Feldman wrote: > My debian/testing system at home also has trouble ray > tracing, especially with sticks. When it fails I get a > segmentation fault. What architecture are you running on? i386 or something else? Do you use pymol's internal raytra

[PyMOL] How to send pymol command to pymol by python interpreter

2004-01-21 Thread Takefumi Sora
Dear Pymol users I launch Pymol in my python program. After that, I can't change objects in pymol in my python program. In short I do not know how to send pymol command (ex cmd.do("show cartoon")) to Pymol not by directly input in pymol external command line but by python interpreter. Does anyb

[PyMOL] Problems with PyMOL + XIG Summit2.2

2004-01-21 Thread Warren L. DeLano
PyMOL Users, It appears that some PyMOL users are having trouble with Xi Graphics' Summit line of OpenGL graphics drivers, version 2.2. Atom picking (which uses glReadPixels with color-encoded pixel buffers) fails with these drivers. It's unclear right now whether the problem is due to the XiG

RE: [PyMOL] How to send pymol command to pymol by python interpreter

2004-01-21 Thread Warren L. DeLano
Takefumi, # If launching PyMOL from an external interpreter, then you need # these two lines first: import pymol pymol.finish_launching() # If using PyMOL directly, then start here... from pymol import cmd # A command like the following cmd.do("show cartoon") # is essentially equivalent to:

[PyMOL] Re: Problems with PyMOL + XIG Summit2.2

2004-01-21 Thread Michael Ginis
Warren, XiG would like to know what is happening with PyMOL and Accelerated-X. We are not experts with PyMOL so we may need help reproducing the problem. WLD>What numeric version of Summit are you using? WLD>What Summit series do you have (LX, DX, CX, WX, etc.)? WLD>What operating system, distro,

Re: [PyMOL] Ray Tracing Crash

2004-01-21 Thread Morri Feldman
Warren, The RH9 Patch fixed the ray tracing problem. Thanks for your help. Tonight I will send you specific information about the Debian ray tracing problem. Thanks, Morri On Wed, 21 Jan 2004 08:07:00 -0800 "Warren L. DeLano" wrote: > Morri, > > The RH9 Patch is described and published on:

[PyMOL] c-alpha traces

2004-01-21 Thread Michal Kurowski
Hi, Some structure comparison software is only able to generate alignments built of c-alpha atoms of both structures compared. Is Pymol able to visualize such alignment with (faked) backbone shown ? If not what could possibly show it ? Regards, -- Michal Kurowski

Re: [PyMOL] Ray Tracing Crash

2004-01-21 Thread Morri Feldman
Regarding my problems raytracing on my debian/testing machine. The system has 128mb of ram. I have attached a pymol session file. To generate the session file, I loaded a very simple molecule into pymol. After loading the session file and executing the ray command I get a segmentation fault.

[PyMOL] translucent proteins

2004-01-21 Thread Lesley Debono
I would like to be able to make the backbone protein in a structure translucent so that the active site is clearly visible through the protein. Any ideas on how to do this? Lesley

RE: [PyMOL] How to send pymol command to pymol by python interpreter

2004-01-21 Thread Takefumi Sora
Hi. I appreciate your answer, Warren. Thank you. Please let me ask one more question. You said I need two lines first: import pymol pymol.finish_launching() As long as I use,I can't the role of "pymol.finish_launching()" if I don't call this, what troubles will happen ? Takefumi SORA