RE: [PyMOL] Pymol script screenplay

2003-10-05 Thread Warren L. DeLano 
Nat,

PyMOL's ray-tracer is pretty simple -- it just divides 3D space up into
equally sized boxes, so that ray-intersection and identification
calculation can be performed rapidly.  The smaller the boxes, the fewer
the number of partial geometries will be present in the box.

Hash_max is a hint to the ray tracer about the maximum number of
subdivisions it should allow on each axis.  In principle, the amount of
RAM used is a 3rd-order function of this value.  However, the ray-tracer
will often use less RAM than that for a variety of reasons.

PyMOL usually ships with hash_max set to 100, since that is reasonable
for a machine with 256 MB of RAM.  300 is about the highest I've tried,
and you could easily require over a Gig of RAM for a situation like
that.  

However, there is definitely a point of diminishing returns, which
depends on scene complexity, total number of pixels, etc.  Typically
each ray-tracing scene will have a different optimum, but usually
140-180 gives the shortest overall rendering times.  

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 Nat Echols
 Sent: Sunday, October 05, 2003 2:28 PM
 To: pymol-users@lists.sourceforge.net
 Subject: RE: [PyMOL] Pymol script screenplay
 
  By the way, you can also use extra RAM to speed up ray-tracing
  by 2-3 fold if you set hash_max to 150-200.
 
 Wait, I'm curious - what does this command do, and what are the
limits?
 For a machine with 2GB of memory, what can I get away with?  Will I
have
 problems if I run multiple invocations of PyMOL at once?
 
 -Nat
 
 
 
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RE: [PyMOL] Pymol script screenplay

2003-10-02 Thread Warren L. DeLano 
Alan,

VMD is more memory efficient that PyMOL.  Probably the main
reason for this is that PyMOL pre-calculates and stores all of the
geometries it is going to show down to the last vertex.  

You can reduce the amount of memory PyMOL needs for cartoons by
setting:

set cartoon_sampling, 3

But the real way to solve your problem is to get more RAM.  If
you're using PyMOL to visualize MD trajectories, I recommend buying as
much RAM as you can afford (and your system can take).  1 GB is a
reasonable minimum.  1.5-2 GB is definitely better.  I don't know what
prices are like in Brazil, but a GB of RAM can be purchased here in the
states for $150-400.

By the way, you can also use extra RAM to speed up ray-tracing
by 2-3 fold if you set hash_max to 150-200.

To answer to your second question:

import os
os.system(mencoder \*.png -mf on:fps=30 -o mvc1ec2.avi
-ovc lavc -lavcopts  vcodec=mpeg4:vbitrate=6000:vhq:keyint=30)

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 Alan Wilter Sousa da Silva
 Sent: Thursday, October 02, 2003 5:32 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Pymol script screenplay
 
 
 Hi List!
 
 I finally got a Pymol script which does what I want, but I still have
 problems.  I follows my actual script:
 
 -
 del all
 mclear
 set cache_frames=0
 set cartoon_fancy_helices, 1
 load c1/forcedin.pdb,c1
 frame 1
 hide all
 run Pymol/stride_ss.py
 stride2pymol c1
 stride2pymol c2
 show sticks, (resi 199)
 show cartoon, all
 color red, c1
 color blue, c2
 set orthoscopic=1
 viewport 640,480
 run Pymol/eixos.py
 translate [18,18,20],object=axes
 run Pymol/cgotext.py
 translate [18,55.5,40],object=txt
 reset
 zoom all,-55
 clip near,2
 mset 1 x10 1 x72 -28 28 x72 28 x10
 util.mroll(11,82,1)
 util.mroll(111,182,1)
 set antialias=1.0
 set ray_trace_frames=1
 mpng png2/mvc1e2
 ---
 
 It works for a 28 frames of MD. But a test.  Extending it for a real
MD
 (~500 frames) I found out that Pymol crashes when command 'show
cartoon,
 all' is running (after done the half of frames, I believe).  Problably
 memory problems, right?  However a similar operation works fine in VMD
 (sorry for comparison). I use a P4 1.6 GHz with 256 Mb Ram.
 
 BTW, how could I insert in Pymol script (python language) such command
 bellow:
 
 mencoder \*.png -mf on:fps=30 -o mvc1ec2.avi -ovc lavc -lavcopts
 vcodec=mpeg4:vbitrate=6000:vhq:keyint=30
 
 
 Thanks in advance for any help.
 
 Cheers,
 
 --
 --
 Alan Wilter Sousa da Silva
 --
 B.Sc. - Dep. Física - UFPA
 M.Sc. - Dep. Física - PUC/RJ
 D.Sc. - IBCCF/UFRJ
 Bolsista Pesquisador LAC-INPE
 São José dos Campos (SP), Brasil
 www.lac.inpe.br/~alan
 
 
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