RE: [PyMOL] set sphere_transparency?

2004-04-14 Thread Warren DeLano
Jason,

The problem is that your script is changing the setting for the specific
object-state by passing it an explicit object name and state number.

   cmd.set( sphere_transparency, str(val), spheres, 0, 1, 1 )

As an important compatibility consideration, I recommend for all API
functions that you only ever pass the specific arguments you need to pass to
API functions, and no others.  In this case, I think that would be:

cmd.set( sphere_transparency, str(val))

which simply changes the global sphere_transparency setting.

That would then make it possible for a subsequent:

   set sphere_transparency, 0

To have the effect you expect.

Cheers,
Warren

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net 
 [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
 Jason Vertrees
 Sent: Tuesday, April 13, 2004 10:28 PM
 To: PyMol Users List
 Subject: [PyMOL] set sphere_transparency?
 
 Hey folks,
 
 Is this a bug or my incorrect usage of PyMol?  (Using 0.95 on 
 a Dual 64-bit Opteron SuSe 9.0 system.)
 
 I used this script (http://vertrees.org/~tree/fade_out.py) to 
 create some images for a my first super-simple movie 
 (http://vertrees.org/~tree/output.mpeg).  
 
 The image (http://vertrees.org/~tree/bad_spheres.png) is the 
 last image the script creates.
 
 The problem is that
   set sphere_transparency, 0
 doesn't seem to work after my script is run.  (The 
 bad_spheres.png above show the command and resulting PyMol 
 model/state.)  So the bad_spheres.png file doesn't respond to 
 'set sphere_transparency, 0'.  
 
 I'm a novice at PyMol and Python scripting, so I'm sure this 
 is my fault instead of PyMol's.
 
 I've tried new selections, enable/disabling things and 
 whatnot. Still sphere's refuse to play nicely.  Oddly enough, 
 'hide spheres' works well.  I've also 'mclear'ed and more.
 
 Any ideas?
 
 Thanks!
 
 -- Jason
 
 -- 
 
 Jason Vertrees
 BSCB Graduate Student @ UTMB, Galveston
 javer...@utmb.edu :: http://www.bscb.utmb.edu
 
 
 ---
 This SF.Net email is sponsored by: IBM Linux Tutorials Free 
 Linux tutorial presented by Daniel Robbins, President and CEO 
 of GenToo technologies. Learn everything from fundamentals to 
 system 
 administration.http://ads.osdn.com/?ad_id=1470alloc_id=3638op=click
 ___
 PyMOL-users mailing list
 PyMOL-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/pymol-users
 





[PyMOL] set sphere_transparency?

2004-04-13 Thread Jason Vertrees
Hey folks,

Is this a bug or my incorrect usage of PyMol?  (Using 0.95 on a Dual
64-bit Opteron SuSe 9.0 system.)

I used this script (http://vertrees.org/~tree/fade_out.py) to create
some images for a my first super-simple movie
(http://vertrees.org/~tree/output.mpeg).  

The image (http://vertrees.org/~tree/bad_spheres.png) is the last image
the script creates.

The problem is that
  set sphere_transparency, 0 
doesn't seem to work after my script is run.  (The bad_spheres.png above
show the command and resulting PyMol model/state.)  So the
bad_spheres.png file doesn't respond to 'set sphere_transparency, 0'.  

I'm a novice at PyMol and Python scripting, so I'm sure this is my fault
instead of PyMol's.

I've tried new selections, enable/disabling things and whatnot. Still
sphere's refuse to play nicely.  Oddly enough, 'hide spheres' works
well.  I've also 'mclear'ed and more.

Any ideas?

Thanks!

-- Jason

-- 

Jason Vertrees
BSCB Graduate Student @ UTMB, Galveston
javer...@utmb.edu :: http://www.bscb.utmb.edu