[PyMOL] Ray Tracing Crash

2004-01-20 Thread Morri Feldman
I am running pymol .93.  When I try to ray trace a scene, the gui shows a 
white status bar that moves halfway across the screen and then freezes.
After this the GUI is frozen and must be killed.  No error messages are
shown.  The computer is running RedHat 9 and has 4 processors.  Has
anyone else experienced this problem?  Do you have any solutions?

This message may double post because I accidentally tried to post it from 
my other email account.  Sorry

Thanks, Morri

Morri Feldman





Re: [PyMOL] Ray Tracing Crash

2004-01-20 Thread Matt Franklin

Morri Feldman wrote:
I am running pymol .93.  When I try to ray trace a scene, the gui shows a 
white status bar that moves halfway across the screen and then freezes.

After this the GUI is frozen and must be killed.  No error messages are
shown.  The computer is running RedHat 9 and has 4 processors.  Has
anyone else experienced this problem?  Do you have any solutions?

This message may double post because I accidentally tried to post it from 
my other email account.  Sorry


Thanks, Morri

Morri Feldman



Hi Morri -

The progress bar for raytracing doesn't move linearly - the first half 
of the bar is covered fairly quickly, then more slowly, then very 
slowly, then the last fifth is usually covered in one jump.  Are you 
sure you just aren't being impatient?  Try raytracing a very simple 
scene, like a single amino acid in spheres mode, to see if it hangs 
then.  Also try raytracing parts of your scene in case some funny bit of 
your molecule is causing this problem.  Finally, try reducing the 
complexity of your surfaces and/or spheres: set surface_quality, -1 (0 
is the default).


Feel free to contact me directly - I'm local!  (Although Warren will be 
more helpful...)


- Matt


--
Matthew FranklinPhone:(650)225-4596
Postdoctoral Researcher   Fax:(650)225-3734
Genentech, Inc.
1 DNA Way, South San Francisco, CA 94080




RE: [PyMOL] Ray Tracing Crash

2004-01-20 Thread Warren L. DeLano
Morri,

(First, thanks Matt for the great diagnostic advice!)

This sounds to me like a potential threading deadlock, possible
due to the broken threading in RedHat 9.  Are you using the stock
version or have you patched glibc?

If you haven't patched your RedHat 9, then one way to be sure
this is the problem is to set max_threads, 1 before issuing the ray
command.  If PyMOL doesn't hang, then you've found the culprit.

If have already patched your RH9, then let's do some more work
to determine what's going on... 

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 Matt Franklin
 Sent: Tuesday, January 20, 2004 6:25 PM
 To: Morri Feldman
 Cc: pymol-users
 Subject: Re: [PyMOL] Ray Tracing Crash
 
 Morri Feldman wrote:
  I am running pymol .93.  When I try to ray trace a scene, the gui
shows
 a
  white status bar that moves halfway across the screen and then
freezes.
  After this the GUI is frozen and must be killed.  No error messages
are
  shown.  The computer is running RedHat 9 and has 4 processors.  Has
  anyone else experienced this problem?  Do you have any solutions?
 
  This message may double post because I accidentally tried to post it
 from
  my other email account.  Sorry
 
  Thanks, Morri
 
  Morri Feldman
 
 
 Hi Morri -
 
 The progress bar for raytracing doesn't move linearly - the first half
 of the bar is covered fairly quickly, then more slowly, then very
 slowly, then the last fifth is usually covered in one jump.  Are you
 sure you just aren't being impatient?  Try raytracing a very simple
 scene, like a single amino acid in spheres mode, to see if it hangs
 then.  Also try raytracing parts of your scene in case some funny bit
of
 your molecule is causing this problem.  Finally, try reducing the
 complexity of your surfaces and/or spheres: set surface_quality, -1
(0
 is the default).
 
 Feel free to contact me directly - I'm local!  (Although Warren will
be
 more helpful...)
 
 - Matt
 
 
 --
 Matthew FranklinPhone:(650)225-4596
 Postdoctoral Researcher   Fax:(650)225-3734
 Genentech, Inc.
 1 DNA Way, South San Francisco, CA 94080
 
 
 
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[PyMOL] controlling atom sphere radii

2004-01-20 Thread rbaxter
Dear All,

I have some residues shown as sticks and a heteroatom shown as a sphere. I woul
dlike to make the sphere a little smaller compared to the sticks. How can I
control the radius of the sphere?

Any help appreciated, snippet of script below,

Richard Baxter

select pocket3=((s;RCVL and i;189,190,212,213,222,223,224))
select fe2=(r;FE2)
...
show sticks,pocket3
show spheres,fe2



Re: [PyMOL] controlling atom sphere radii

2004-01-20 Thread Michael George Lerner
to make all spheres smaller, try something like this:

set sphere_scale, 0.3

play around with the 0.3 bit to get the size you want.

last time i checked, you could only have one sphere_scale per object, so
if you want different sized spheres in the same picture (i don't think you
do), you may need to do something like this:

# show normal spheres for ARGs
show spheres, resn arg
# show small spheres for ILEs
create iles, resn ile
show spheres, iles
set sphere_scale, 0.3, iles

(i'm on a windows box with an old version of PyMOL right now, so i don't
know if that last bit has changed recently)

-michael

--
This isn't a democracy;|_  |Michael Lerner
 it's a cheer-ocracy.  | ASCII ribbon campaign ( ) |   Michigan
-Torrence,  Bring It On|  - against HTML email  X  |  Biophysics
   |   / \ | mler...@umich

On Tue, 20 Jan 2004 rbax...@uchicago.edu wrote:

 Dear All,

 I have some residues shown as sticks and a heteroatom shown as a sphere.
 I woul dlike to make the sphere a little smaller compared to the sticks.
 How can I control the radius of the sphere?

 Any help appreciated, snippet of script below,

 Richard Baxter

 select pocket3=((s;RCVL and i;189,190,212,213,222,223,224))
 select fe2=(r;FE2)
 ...
 show sticks,pocket3
 show spheres,fe2


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 The SF.Net email is sponsored by EclipseCon 2004
 Premiere Conference on Open Tools Development and Integration
 See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
 http://www.eclipsecon.org/osdn
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