Re: [PyMOL] Problem with distutils build 3951 on Ubuntu Lucid 10.04 : X Error of failed request: BadRequest

2011-06-08 Thread Jason Vertrees
Hari,

>  Hit ESC anytime to toggle between text and graphics.
>  Detected OpenGL version 2.0 or greater.  Shaders available.
> X Error of failed request:  BadRequest (invalid request code or no such
> operation)
>   Major opcode of failed request:  128 (GLX)
>   Minor opcode of failed request:  169 ()
>   Serial number of failed request:  46
>   Current serial number in output stream:  46

This sounds like a driver problem.  Can you run the 'glxgears'
program?  Does it give the same error?  Do you have the latest driver
installed?

Cheers,

-- Jason

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Re: [PyMOL] problems cloring sticks

2011-06-08 Thread Jason Vertrees
For those using a more recent version of PyMOL (v1.4+) who have this
stick coloring problem, can you please try:

set use_shaders, 1

and let me know if that fixes the stick rendering issue?  We've
located the bug and are looking for a suitable workaround.  (The
colors are being set properly, but the video card isn't picking them
up.)

Cheers,

-- Jason

On Wed, Jun 1, 2011 at 12:04 PM, Ariel Talavera  wrote:
> Hi Pymolers,
>
> I am having problems coloring residues when they are shown as stick. The
> coloring is properly working for the other representations like, lines,
> surface or spheres. I am using Pymol 1.2r2 under Ubuntu 11,04.
>
> Thanks in advanced,
> best regrads,
> Ariel
>
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[PyMOL] Problem with distutils build 3951 on Ubuntu Lucid 10.04 : X Error of failed request: BadRequest

2011-06-08 Thread hari jayaram
Hi I just build the svn build of pymol 3951 on 64 bit Ubuntu Lucid  .
I first had to  installing libglew and libglew-dev after which the build
progressed fine , but when I run the built pymol I get the following errors
( below)  and pymol does not launch.

I tried with a clean repo checked out from svn and get the same error. I
also tried the makefile route but get a cetypes.h include error.
I know the distutils way is the recommended approach..

Any help to resurrect my pymol will be greatly appreciated.

Thanks
Hari

 hari@hari:~/pymol-read-only/trunk/pymol$ ./pymol
 PyMOL(TM) Molecular Graphics System, Version 1.4.1.
 Copyright (c) Schrodinger, LLC.
 All Rights Reserved.

Created by Warren L. DeLano, Ph.D.

PyMOL is user-supported open-source software.  Although some versions
are freely available, PyMOL is not in the public domain.

If PyMOL is helpful in your work or study, then please volunteer
support for our ongoing efforts to create open and affordable scientific
software by purchasing a PyMOL Maintenance and/or Support subscription.

More information can be found at "http://www.pymol.org";.

Enter "help" for a list of commands.
Enter "help " for information on a specific command.

 Hit ESC anytime to toggle between text and graphics.

 Detected OpenGL version 2.0 or greater.  Shaders available.
X Error of failed request:  BadRequest (invalid request code or no such
operation)
  Major opcode of failed request:  128 (GLX)
  Minor opcode of failed request:  169 ()
  Serial number of failed request:  46
  Current serial number in output stream:  46
 PyMOL: abrupt program termination.

Thanks
hari
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Re: [PyMOL] surface display in new pymol

2011-06-08 Thread Luca Jovine
Hi Venki,

You need to first issue the following command:

set surface_mode, 1

Best, Luca

On Jun 8, 2011, at 17:05 , V. Ramakrishnan wrote:

> On versions 1.3, 1.4, I cannot display a surface of anything that is not in 
> the standard dictionary. For example trying to draw a surface of tRNA shows 
> gaps in the modified bases. Drawing a surface of a ligand such as an 
> antibiotic similarly is just a blank. This was not true in the older 
> versions, e.g. 0.98 or 0.99.
> I'm using Mac OS X 10.6.7
> Does anyone else have this problem and is there a way around it?
> 
> Thanks,
> Venki
> 
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[PyMOL] surface display in new pymol

2011-06-08 Thread V. Ramakrishnan
On versions 1.3, 1.4, I cannot display a surface of anything that is not in the 
standard dictionary. For example trying to draw a surface of tRNA shows gaps in 
the modified bases. Drawing a surface of a ligand such as an antibiotic 
similarly is just a blank. This was not true in the older versions, e.g. 0.98 
or 0.99.
I'm using Mac OS X 10.6.7
Does anyone else have this problem and is there a way around it?

Thanks,
Venki


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[PyMOL] Pymol crashing when executed on Windows 7_64Bit

2011-06-08 Thread Greipel.Joachim
Hi,
 
We have some computers with Windows 7, 64 Bit installed. When invoking Pymol
(incentive) Version 1.4  or 1.4.1 it crashes immediately giving the
following error output:
 
Faulting application name: pymol.exe, version: 0.0.0.0, time stamp:
0x4d85901b
Faulting module name: pymol.exe, version: 0.0.0.0, time stamp: 0x4d85901b
Exception code: 0xc005
Fault offset: 0x0001ed86
Faulting process id: 0x25a8
Faulting application start time: 0x01cc2506140daba7
Faulting application path: Q:\apps\pymol\1.4\pymol.exe
Faulting module path: Q:\apps\pymol\1.4\pymol.exe
Report Id: 54d45971-90f9-11e0-9553-001d60e011a1

This is independent of using the 64- or 32-bit version of pymol. We had to
revert to Version 1.2, which is working. Does anyone have an advice?
 
Regards,
 
Joachim Greipel
 
 
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