[PyMOL] Transparent cartoons?

2003-09-15 Thread Christian Siebold

Dear Pymol users

How can I create transparent cartoon?
I tried to use the transparency option from the setting panel, but 
this only worked for surfaces and not for cartoons.


Thanks a lot,
Christian


--
Dr. Christian Siebold
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
University of Oxford
Roosevelt Drive, Oxford OX3 7BN, UK

Tel: (+44)-1865-287550
Fax: (+44)-1865-287547
Email: christ...@strubi.ox.ac.uk
Website: http://www.strubi.ox.ac.uk




RE: [PyMOL] Transparent cartoons?

2003-09-15 Thread Warren L. DeLano
Christian,

Transparent cartoons have been implemented, but not yet released
excepted in the latest G4/G5 Mac demo version.  If you have a Mac, you
can 

set cartoon_transparency, 0.5

using that version.  Note that cartoon transparency is really only
useful when ray-tracing, because visual artifacts will occur with
standard OpenGL rendering.

If you're on a PC, then you'll need to wait for the next big
release, which will probably happen next week.

Cheers,
Warren


--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Christian Siebold
 Sent: Monday, September 15, 2003 10:11 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Transparent cartoons?
 
 Dear Pymol users
 
 How can I create transparent cartoon?
 I tried to use the transparency option from the setting panel, but
 this only worked for surfaces and not for cartoons.
 
 Thanks a lot,
 Christian
 
 
 --
 Dr. Christian Siebold
 Division of Structural Biology
 Wellcome Trust Centre for Human Genetics
 University of Oxford
 Roosevelt Drive, Oxford OX3 7BN, UK
 
 Tel: (+44)-1865-287550
 Fax: (+44)-1865-287547
 Email: christ...@strubi.ox.ac.uk
 Website: http://www.strubi.ox.ac.uk
 
 
 
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RE: [PyMOL] pymol raytracing crash

2003-09-15 Thread Warren L. DeLano
Thomas,

I tried running your script on the current development version
and on a version 0.90 binary, and wasn't able to get PyMOL to crash.

How is PyMOL installed on your system?

Cheers,
Warren

--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Thomas Siegmund
 Sent: Wednesday, September 10, 2003 6:16 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] pymol raytracing crash
 


 Hi everybody,
 
 I am new to pymol. So maybe I'm doing something wrong, but pymol
almost
 everytime crashes when I try to raytrace a picture. I had some success
 with
 small protein structures in cartoon representation. The same molecule
in
 lines or sticks representation crashes the pymol raytracer.
 
 Here some console output:
 
 siegm...@siegmund:~ /usr/local/bin/python
 /usr/local/lib/python2.3/site-packages/pymol/__init__.py -x
 /tmp/pymol/7LYZ.pdb
 
  PyMOL(TM) Molecular Graphics System, Version 0.90.
  Copyright (C) 1998-2003 by DeLano Scientific LLC.
 // I cut some lines here
  OpenGL based graphics front end:
   GL_VENDOR: NVIDIA Corporation
   GL_RENDERER: RIVA TNT2/AGP/SSE2
   GL_VERSION: 1.4.0 NVIDIA 44.96
  PDBStrToCoordSet: Attempting to read symmetry information
  Crystal: Unit Cell   27.400   31.900   34.400
  Crystal: Alpha Beta Gamma88.000  108.000  112.000
  Crystal: RealToFrac Matrix
  Crystal:0.03650.01470.0133
  Crystal:0.0.03380.0031
  Crystal:0.0.0.0307
  Crystal: FracToReal Matrix
  Crystal:   27.4000  -11.9500  -10.6302
  Crystal:0.   29.5772   -3.
  Crystal:0.0.   32.5785
  Crystal: Unit Cell Volume26402.
  Symmetry:  1.0  0.0  0.0  0.0
  Symmetry:  0.0  1.0  0.0  0.0
  Symmetry:  0.0  0.0  1.0  0.0
  Symmetry:  0.0  0.0  0.0  1.0
  Executive: object 7LYZ created.
 PyMOLutil.ss
  util.ss: WARNING: This is not a correct secondary structure
 // I cut some lines here
  util.ss: assignment complete.
 PyMOLhide lines
 PyMOLshow cartoon
 PyMOLray
  Ray: total time: 1.14 sec. = 3145.7 frames/hour. (1.15 sec. accum.)
 PyMOLhide cartoon
 PyMOLshow sticks
 PyMOLray
 Speicherzugriffsfehler (segmentation fault)
 
 Pymol is version 0.9, installed from source package on SuSE linux 8.2.
To
 make
 sure that it is not a problem of the python installation (standard
SuSE
 8.2
 rpm, python-2.2.2) I installed python 2.3 from source. Same result. In
the
 mailing list archive I found comments about memory usage for
raytracing.
 This
 machine has 500 MB RAM. Top shows about 150-200 MB free RAM and 1GB
 untouched
 swap just before the raytracing. I tried the command set hash_max,
60 as
 recommended, but this also did not help.
 
 Any hints?
 
 Tanks for your help
 
 Thomas
 
 --
 Thomas Siegmund, Ph.D.
 DeveloGen AG
 Bioinformatics and Data Management
 Phone: +49(551) 505 58 651
 
 
 
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