Hi,
 
Did someone compile pymol successfully on core3 ? 
My uname -a is
Linux protein 2.6.8-1.541 #1 Wed Sep 1 18:01:20 EDT 2004 i686 athlon i386 GNU/Linux .

I just tried to install pymol in my fedora core3 test3 OS.




Other Unix
  1. Download the source: pymol-0_97-src.tgz (alternate).
  2. Either configure PyMOL to use your existing external dependencies, or download and compile from sources:
    ext-0_95-src.tgz (alternate) includes:
  3. Compile pymol (see INSTALL file for details).





在 2004-11-23二的 20:45 -0800,pymol-users-request@lists.sourceforge.net写道:
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Today's Topics:

   1. Re: List participation commentary (Kristian Rother)
   2. 0.98 beta 18 Selecting bug (Jules Jacobsen)
   3. PyMol not displaying molecules (Greg Landrum)
   4. Re: PyMol not displaying molecules (Greg Landrum)

--__--__--

Message: 1
From: Kristian Rother <kristian.rother@charite.de>
Organization: Charite Berlin
To: pymol-users@lists.sourceforge.net
Date: Tue, 23 Nov 2004 07:58:58 +0000
Subject: [PyMOL] Re: List participation commentary

On Monday 22 November 2004 18:49, Cameron Mura wrote:
> >Ultimately the mailing list serves as a form of living manual to the
> > program, so it would be nice to preserve as many of these insights as
> > possible!

Well, i have written up and sorted a number of answers to common problems o=
n=20
my homepage. However, it's far away from being a wiki. Neither it is comple=
te=20
in any way.

http://www.rubor.de/bioinf/pymol_tips.html

Yours,

   Kristian Rother
   Humboldt Universit=E4t Berlin


--__--__--

Message: 2
Date: Tue, 23 Nov 2004 11:26:43 +0000
From: Jules Jacobsen <jobj2@hermes.cam.ac.uk>
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] 0.98 beta 18 Selecting bug

Oops! sorry, I just realized that the .pse was quite large. My apologies.

The pdbs used were 1hju, 1hjs and 1hjq. The following script will 
produce the same pse:

select Binding, (resi 86,300)
label Binding and elem o, (resn+'-'+resi)
zoom Binding


Jules

-------- Original Message --------
Subject: 0.98 beta 18 Selecting
Date: Tue, 23 Nov 2004 11:05:01 +0000
From: Jules Jacobsen <jobj2@hermes.cam.ac.uk>
To: pymol-users@lists.sourceforge.net

Hi all,

Has anyone else had the problem of not being able to select several
identical residue types in aligned structures? eg in the .pse included,
if you single left-click on Trp-86 (the left one of the 'Binding'
selection) and try to select them all in the same manner, PyMOL won't
add any more residues to the selection if it has the same resn/resi. It
will select them if you use a shift-left-click. It will however, happily
remove them from the selection with a single left-click.

I'm guessing this is a PyMOL rather than platform specific bug? (I'm
running on WinXP)

Cheers,

Jules




--__--__--

Message: 3
Date: Tue, 23 Nov 2004 17:11:54 -0800
To: pymol-users@lists.sourceforge.net
From: Greg Landrum <greglandrum@earthlink.net>
Subject: [PyMOL] PyMol not displaying molecules


I've encountered a problem where PyMol will no longer display molecules 
using normal rendering on my machine.  (Symptoms: I load a molecule and see 
nothing, but if I raytrace the image, the result looks fine).  I've 
verified that this happens in pymol versions 0.97 and 0.98beta18.

System details:
OS: Win2K
Graphics Card: Radeon 7000 series
Graphics Driver: the most recent ATI driver suite (6.14.10.6483).

I'm not 100% certain, but I am pretty sure that the problem dates to my 
update of the graphics driver.  Any suggestions as to how I might work 
around this problem?

Here's PyMol's startup output, in case that's useful:

  PyMOL(TM) Molecular Graphics System, Version 0.98beta18.
  Copyright (C) 2004 by DeLano Scientific LLC.
  All Rights Reserved.

     Created by Warren L. DeLano, Ph.D.

     Other Major Authors and Contributors:

        Ralf W. Grosse-Kunstleve, Ph.D.

     PyMOL is user-supported open-source software.  Although most 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 campaign to create open and affordable software
     for molecular research.

     Updates and other information can be found at "http://www.pymol.org".

     Please cite PyMOL in publications and presentations:

        Warren L. DeLano "The PyMOL Molecular Graphics System."
        DeLano Scientific LLC, San Carlos, CA, USA. http://www.pymol.org

     Enter "help" for a list of commands.
     Enter "help <command-name>" for information on a specific command.

  Hit ESC anytime to toggle between text and graphics.

  OpenGL-based graphics engine:
   GL_VENDOR: ATI Technologies Inc.
   GL_RENDERER: RADEON 7000 DDR x86/SSE2
   GL_VERSION: 1.3.4650 Win2000 Release

Thanks in advance for any help,
-greg

----
greg Landrum (greglandrum@earthlink.net)
Software Carpenter/Computational Chemist



--__--__--

Message: 4
Date: Tue, 23 Nov 2004 20:08:33 -0800
To: pymol-users@lists.sourceforge.net
From: Greg Landrum <greglandrum@earthlink.net>
Subject: Re: [PyMOL] PyMol not displaying molecules

At 05:11 PM 11/23/2004, I wrote:

>I'm not 100% certain, but I am pretty sure that the problem dates to my 
>update of the graphics driver.  Any suggestions as to how I might work 
>around this problem?

For what it's worth, when I go back to an older version of the ATI driver 
(6.14.10.6343, dated 4/28/2003), everything works fine.

-greg

----
greg Landrum (greglandrum@earthlink.net)
Software Carpenter/Computational Chemist




--__--__--

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