Well, it took only a couple of hours (1+ days) to figure this out.
Scratch the real problem.
It turned out to be a stale and conflicting installation of python2.4 that I was not aware of. After removing the mess, pymol compiles without any issues and works just fine. That was clearly a real problem - for me and my machine :-)

DeLano Scientific wrote:

Unfortunately, you are not the first to report trouble on FC6, so this is
clearly real problem.  

However, with our 64-bit FC6 install, PyMOL works fine -- and others have
reported success as well.  In other words, there is some problem here other
than simply, 64 bit + FC6 + PyMOL, but as of yet, no one has figured out
what it is...

The freeglut error is a separate cause for concern.  That means you do not
have compatible vendor-supplied OpenGL drivers installed, and thus, PyMOL
will run rather slowly.

As for 64-bit, there are no official 64-bit builds yet, but source code can
definitely be built in 64-bit mode on Linux.


-----Original Message-----
From: pymol-users-bounces@lists.sourceforge.net 
[mailto:pymol-users-bounces@lists.sourceforge.net] On Behalf 
Of gerwald jogl
Sent: Friday, May 11, 2007 10:57 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] frozen command line on amd64


Pymol is behaving interestingly on my amd64 dual core, fedora 
core6 updated, python2.4.

I have tried the precompiled version 0.99rev9 and the latest 
beta for linux-32bit and the only 64-bit I could see dated may 2006.

The binary comes up as usual, but the tcl command line is 
frozen and will not accept any keyport input. That's 
obviously not helpful.

I wonder if someone else has seen this behavior or has ideas 
how to go about it.


below more detailed info...

this is the pymol output on startup, note the freeglut error:

freeglut (/xsoft/pymol-0.99rev9/pymol.exe): Unable to create 
direct context rend ering for window 'PyMOL Viewer'
This may hurt performance.
 PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano 
Scientific LLC.
 This PyMOL Executable Build is exclusively available to 
PyMOL Sponsors  with current PyMOL Maintenance and/or Support 
Subscriptions.  Only  designated PyMOL Power, Casual, and 
Developer Users covered within the  scope of such a 
Subscription may legally use this software product.
 Any other usage is specifically prohibited and may 
constitute a  violation of United States and international 
Copyright laws.
 This Executable Build integrates and extends Open-Source 
PyMOL 0.99rev9.
 OpenGL graphics engine:
  GL_VENDOR: NVIDIA Corporation
  GL_VERSION: 1.4 (2.1.0 NVIDIA 97.55)
 Adapting to GeForce hardware.
 Detected 2 CPUs.  Enabled multithreaded rendering.

In addition (no I don't really have ample time to spend on 
this), here is how far the simple-minded approach to compile 
the source code leads on this machine:
Comments on this would also be appreciated :-)

This is the output from: python setup.py build.

gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall 
-Wstrict-prototypes -fPI C -D_PYMOL_MODULE -D_PYMOL_INLINE 
-D_PYMOL_FREETYPE -D_HAVE_LIBPNG -Iov/src -Ila yer0 -Ilayer1 
-Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5
-I/usr/include/freetype2 -I/us
r/local/include/python2.4 -c layer1/PConv.c -o 
build/temp.linux-x86_64-2.4/layer 1/PConv.o -ffast-math 
-funroll-loops -O3 In file included from 
                 from layer0/os_python.h:28,
                 from layer1/PConv.c:18:
/usr/local/include/python2.4/pyport.h:612:2: error: #error 
"LONG_BIT definition appears wrong for platform (bad 
gcc/glibc config?)."
error: command 'gcc' failed with exit status 1

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