Re: [PyMOL] Problems with Pymol 1.4.1 under Ubuntu 11.04

2011-06-10 Thread Bernhard Lechtenberg 
Hello all,

I finally solved the problem by updating my video drivers to the most up
to date drivers from the xorg edgers project. I think they're rather
experimental but seem to work nicely for me so far.

Thanks for all the helpful suggestions.

Bernhard

-Original Message-
From: Bernhard Lechtenberg bc...@cam.ac.uk
To: Jason Vertrees jason.vertr...@schrodinger.com
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Problems with Pymol 1.4.1 under Ubuntu 11.04
Date: Thu, 09 Jun 2011 21:31:58 +0100

Jason,

clicking inside the window does not have any effect. I can't even close
the window, other than terminating the terminal I started it from. The
only thing that works is minimizing and moving the window around on the
desktop.

I just compiled pymol 1.4.1 on my home computer which also runs Ubuntu
11.04 and also has an Intel Graphics card and everything seems to be
alright here. Only difference I can think of is that the home computer
has an older Intel graphics board, which only supports an OpenGL version
prior to 2.0, hence the shaders and volumes in pymol are unavailable.
Not sure if that could be the difference.

Thanks,
Bernhard


Am Donnerstag, den 09.06.2011, 16:00 -0400 schrieb Jason Vertrees:
 Hi Bernhard,
 
 I just compiled and installed PyMOL v1.4.1 on Ubuntu 11.04 on using a
 virtual machine (Parallels).  PyMOL worked fine except for some some
 goofy rendering artifacts when you move the PyMOL window around.
 Those artifacts go away when you click inside the window to resume
 PyMOL. I believe these artifacts are due to the unity system or the
 Parallels OpenGL drivers.
 
 Does clicking inside the openGL window resume PyMOL or is PyMOL just frozen?
 
 Also, I just pushed a change that includes better rendering for
 volumes.  This helped quite a bit on my VM.
 
 Cheers,
 
 -- Jason
 
 On Thu, Jun 9, 2011 at 12:04 PM, Bernhard Lechtenberg bc...@cam.ac.uk wrote:
  Hello Jason
 
  all desktop effects should have been turned off, but just too make sure
  I started Ubuntu with the option 'Ubuntu Classic - no effects' but the
  problem with pymol still persists.
 
  Do you have any other ideas?
 
  Thanks,
  Bernhard
 
  -Original Message-
  From: Jason Vertrees jason.vertr...@schrodinger.com
  To: Bernhard Lechtenberg bc...@cam.ac.uk
  Cc: pymol-users@lists.sourceforge.net
  Subject: Re: [PyMOL] Problems with Pymol 1.4.1 under Ubuntu 11.04
  Date: Thu, 9 Jun 2011 11:24:27 -0400
 
  Bernhard,
 
  Do you have desktop effects (aka compositing) turned on?  If so,
  please turn it off and try PyMOL again.
 
  Cheers,
 
  -- Jason
 
  On Thu, Jun 9, 2011 at 9:53 AM, Bernhard Lechtenberg bc...@cam.ac.uk 
  wrote:
  Dear Pymol users
 
  because I had the stick coloring problem with my Intel graphics board, I
  just compiled Pymol 1.4.1 under Ubuntu 11.04 (had some problems there
  and had to change from gcc4.5 to gcc4.4, but it then worked). However,
  now I have another problem after starting pymol. The main Pymol Viewer
  window pops up after starting pymol, but I don't see anything other than
  the outer frame of the window with just a snapshot of the Desktop
  background in the center. The other pymol window does not appear at all
  and there are no error messages in the terminal, it only shows:
 
   PyMOL(TM) Molecular Graphics System, Version 1.4.1.
   Copyright (c) Schrodinger, LLC.
   All Rights Reserved.
  {...cut out ...}
   Detected OpenGL version 2.0 or greater.  Shaders available.
 
  I did not have those problems with pymol 1.3.
 
  Any suggestions how to solve this problem would be highly appreciated.
 
  Thanks,
  Bernhard
 
 
  --
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[PyMOL] Problems with Pymol 1.4.1 under Ubuntu 11.04

2011-06-09 Thread Bernhard Lechtenberg 
Dear Pymol users

because I had the stick coloring problem with my Intel graphics board, I
just compiled Pymol 1.4.1 under Ubuntu 11.04 (had some problems there
and had to change from gcc4.5 to gcc4.4, but it then worked). However,
now I have another problem after starting pymol. The main Pymol Viewer
window pops up after starting pymol, but I don't see anything other than
the outer frame of the window with just a snapshot of the Desktop
background in the center. The other pymol window does not appear at all
and there are no error messages in the terminal, it only shows:

 PyMOL(TM) Molecular Graphics System, Version 1.4.1.
 Copyright (c) Schrodinger, LLC.
 All Rights Reserved.
{...cut out ...}
 Detected OpenGL version 2.0 or greater.  Shaders available.

I did not have those problems with pymol 1.3.

Any suggestions how to solve this problem would be highly appreciated.

Thanks,
Bernhard


--
EditLive Enterprise is the world's most technically advanced content
authoring tool. Experience the power of Track Changes, Inline Image
Editing and ensure content is compliant with Accessibility Checking.
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Re: [PyMOL] Problems with Pymol 1.4.1 under Ubuntu 11.04

2011-06-09 Thread Jason Vertrees 
Bernhard,

Do you have desktop effects (aka compositing) turned on?  If so,
please turn it off and try PyMOL again.

Cheers,

-- Jason

On Thu, Jun 9, 2011 at 9:53 AM, Bernhard Lechtenberg bc...@cam.ac.uk wrote:
 Dear Pymol users

 because I had the stick coloring problem with my Intel graphics board, I
 just compiled Pymol 1.4.1 under Ubuntu 11.04 (had some problems there
 and had to change from gcc4.5 to gcc4.4, but it then worked). However,
 now I have another problem after starting pymol. The main Pymol Viewer
 window pops up after starting pymol, but I don't see anything other than
 the outer frame of the window with just a snapshot of the Desktop
 background in the center. The other pymol window does not appear at all
 and there are no error messages in the terminal, it only shows:

  PyMOL(TM) Molecular Graphics System, Version 1.4.1.
  Copyright (c) Schrodinger, LLC.
  All Rights Reserved.
 {...cut out ...}
  Detected OpenGL version 2.0 or greater.  Shaders available.

 I did not have those problems with pymol 1.3.

 Any suggestions how to solve this problem would be highly appreciated.

 Thanks,
 Bernhard


 --
 EditLive Enterprise is the world's most technically advanced content
 authoring tool. Experience the power of Track Changes, Inline Image
 Editing and ensure content is compliant with Accessibility Checking.
 http://p.sf.net/sfu/ephox-dev2dev
 ___
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

--
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Re: [PyMOL] Problems with Pymol 1.4.1 under Ubuntu 11.04

2011-06-09 Thread Bernhard Lechtenberg 
Hello Jason

all desktop effects should have been turned off, but just too make sure
I started Ubuntu with the option 'Ubuntu Classic - no effects' but the
problem with pymol still persists.

Do you have any other ideas?

Thanks,
Bernhard

-Original Message-
From: Jason Vertrees jason.vertr...@schrodinger.com
To: Bernhard Lechtenberg bc...@cam.ac.uk
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Problems with Pymol 1.4.1 under Ubuntu 11.04
Date: Thu, 9 Jun 2011 11:24:27 -0400

Bernhard,

Do you have desktop effects (aka compositing) turned on?  If so,
please turn it off and try PyMOL again.

Cheers,

-- Jason

On Thu, Jun 9, 2011 at 9:53 AM, Bernhard Lechtenberg bc...@cam.ac.uk wrote:
 Dear Pymol users

 because I had the stick coloring problem with my Intel graphics board, I
 just compiled Pymol 1.4.1 under Ubuntu 11.04 (had some problems there
 and had to change from gcc4.5 to gcc4.4, but it then worked). However,
 now I have another problem after starting pymol. The main Pymol Viewer
 window pops up after starting pymol, but I don't see anything other than
 the outer frame of the window with just a snapshot of the Desktop
 background in the center. The other pymol window does not appear at all
 and there are no error messages in the terminal, it only shows:

  PyMOL(TM) Molecular Graphics System, Version 1.4.1.
  Copyright (c) Schrodinger, LLC.
  All Rights Reserved.
 {...cut out ...}
  Detected OpenGL version 2.0 or greater.  Shaders available.

 I did not have those problems with pymol 1.3.

 Any suggestions how to solve this problem would be highly appreciated.

 Thanks,
 Bernhard


 --
 EditLive Enterprise is the world's most technically advanced content
 authoring tool. Experience the power of Track Changes, Inline Image
 Editing and ensure content is compliant with Accessibility Checking.
 http://p.sf.net/sfu/ephox-dev2dev
 ___
 PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
 Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net






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Editing and ensure content is compliant with Accessibility Checking.
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Re: [PyMOL] Problems with Pymol 1.4.1 under Ubuntu 11.04

2011-06-09 Thread Jason Vertrees 
Hi Bernhard,

I just compiled and installed PyMOL v1.4.1 on Ubuntu 11.04 on using a
virtual machine (Parallels).  PyMOL worked fine except for some some
goofy rendering artifacts when you move the PyMOL window around.
Those artifacts go away when you click inside the window to resume
PyMOL. I believe these artifacts are due to the unity system or the
Parallels OpenGL drivers.

Does clicking inside the openGL window resume PyMOL or is PyMOL just frozen?

Also, I just pushed a change that includes better rendering for
volumes.  This helped quite a bit on my VM.

Cheers,

-- Jason

On Thu, Jun 9, 2011 at 12:04 PM, Bernhard Lechtenberg bc...@cam.ac.uk wrote:
 Hello Jason

 all desktop effects should have been turned off, but just too make sure
 I started Ubuntu with the option 'Ubuntu Classic - no effects' but the
 problem with pymol still persists.

 Do you have any other ideas?

 Thanks,
 Bernhard

 -Original Message-
 From: Jason Vertrees jason.vertr...@schrodinger.com
 To: Bernhard Lechtenberg bc...@cam.ac.uk
 Cc: pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] Problems with Pymol 1.4.1 under Ubuntu 11.04
 Date: Thu, 9 Jun 2011 11:24:27 -0400

 Bernhard,

 Do you have desktop effects (aka compositing) turned on?  If so,
 please turn it off and try PyMOL again.

 Cheers,

 -- Jason

 On Thu, Jun 9, 2011 at 9:53 AM, Bernhard Lechtenberg bc...@cam.ac.uk wrote:
 Dear Pymol users

 because I had the stick coloring problem with my Intel graphics board, I
 just compiled Pymol 1.4.1 under Ubuntu 11.04 (had some problems there
 and had to change from gcc4.5 to gcc4.4, but it then worked). However,
 now I have another problem after starting pymol. The main Pymol Viewer
 window pops up after starting pymol, but I don't see anything other than
 the outer frame of the window with just a snapshot of the Desktop
 background in the center. The other pymol window does not appear at all
 and there are no error messages in the terminal, it only shows:

  PyMOL(TM) Molecular Graphics System, Version 1.4.1.
  Copyright (c) Schrodinger, LLC.
  All Rights Reserved.
 {...cut out ...}
  Detected OpenGL version 2.0 or greater.  Shaders available.

 I did not have those problems with pymol 1.3.

 Any suggestions how to solve this problem would be highly appreciated.

 Thanks,
 Bernhard


 --
 EditLive Enterprise is the world's most technically advanced content
 authoring tool. Experience the power of Track Changes, Inline Image
 Editing and ensure content is compliant with Accessibility Checking.
 http://p.sf.net/sfu/ephox-dev2dev
 ___
 PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
 Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net









-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

--
EditLive Enterprise is the world's most technically advanced content
authoring tool. Experience the power of Track Changes, Inline Image
Editing and ensure content is compliant with Accessibility Checking.
http://p.sf.net/sfu/ephox-dev2dev
___
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Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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Re: [PyMOL] Problems with Pymol 1.4.1 under Ubuntu 11.04

2011-06-09 Thread Bernhard Lechtenberg 
Jason,

clicking inside the window does not have any effect. I can't even close
the window, other than terminating the terminal I started it from. The
only thing that works is minimizing and moving the window around on the
desktop.

I just compiled pymol 1.4.1 on my home computer which also runs Ubuntu
11.04 and also has an Intel Graphics card and everything seems to be
alright here. Only difference I can think of is that the home computer
has an older Intel graphics board, which only supports an OpenGL version
prior to 2.0, hence the shaders and volumes in pymol are unavailable.
Not sure if that could be the difference.

Thanks,
Bernhard


Am Donnerstag, den 09.06.2011, 16:00 -0400 schrieb Jason Vertrees:
 Hi Bernhard,
 
 I just compiled and installed PyMOL v1.4.1 on Ubuntu 11.04 on using a
 virtual machine (Parallels).  PyMOL worked fine except for some some
 goofy rendering artifacts when you move the PyMOL window around.
 Those artifacts go away when you click inside the window to resume
 PyMOL. I believe these artifacts are due to the unity system or the
 Parallels OpenGL drivers.
 
 Does clicking inside the openGL window resume PyMOL or is PyMOL just frozen?
 
 Also, I just pushed a change that includes better rendering for
 volumes.  This helped quite a bit on my VM.
 
 Cheers,
 
 -- Jason
 
 On Thu, Jun 9, 2011 at 12:04 PM, Bernhard Lechtenberg bc...@cam.ac.uk wrote:
  Hello Jason
 
  all desktop effects should have been turned off, but just too make sure
  I started Ubuntu with the option 'Ubuntu Classic - no effects' but the
  problem with pymol still persists.
 
  Do you have any other ideas?
 
  Thanks,
  Bernhard
 
  -Original Message-
  From: Jason Vertrees jason.vertr...@schrodinger.com
  To: Bernhard Lechtenberg bc...@cam.ac.uk
  Cc: pymol-users@lists.sourceforge.net
  Subject: Re: [PyMOL] Problems with Pymol 1.4.1 under Ubuntu 11.04
  Date: Thu, 9 Jun 2011 11:24:27 -0400
 
  Bernhard,
 
  Do you have desktop effects (aka compositing) turned on?  If so,
  please turn it off and try PyMOL again.
 
  Cheers,
 
  -- Jason
 
  On Thu, Jun 9, 2011 at 9:53 AM, Bernhard Lechtenberg bc...@cam.ac.uk 
  wrote:
  Dear Pymol users
 
  because I had the stick coloring problem with my Intel graphics board, I
  just compiled Pymol 1.4.1 under Ubuntu 11.04 (had some problems there
  and had to change from gcc4.5 to gcc4.4, but it then worked). However,
  now I have another problem after starting pymol. The main Pymol Viewer
  window pops up after starting pymol, but I don't see anything other than
  the outer frame of the window with just a snapshot of the Desktop
  background in the center. The other pymol window does not appear at all
  and there are no error messages in the terminal, it only shows:
 
   PyMOL(TM) Molecular Graphics System, Version 1.4.1.
   Copyright (c) Schrodinger, LLC.
   All Rights Reserved.
  {...cut out ...}
   Detected OpenGL version 2.0 or greater.  Shaders available.
 
  I did not have those problems with pymol 1.3.
 
  Any suggestions how to solve this problem would be highly appreciated.
 
  Thanks,
  Bernhard
 
 
  --
  EditLive Enterprise is the world's most technically advanced content
  authoring tool. Experience the power of Track Changes, Inline Image
  Editing and ensure content is compliant with Accessibility Checking.
  http://p.sf.net/sfu/ephox-dev2dev
  ___
  PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
  Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
  Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
 
 
 
 
 
 
 
 
 



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Editing and ensure content is compliant with Accessibility Checking.
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