RE: [PyMOL] Pymol script screenplay

[Warren L. D. <wa...@de...>]

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. =20

	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=3D30 -o mvc1ec2.avi
-ovc lavc -lavcopts > vcodec=3Dmpeg4:vbitrate=3D6000:vhq:keyint=3D30")

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154=20
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of Alan Wilter Sousa da Silva
> Sent: Thursday, October 02, 2003 5:32 AM
> To: pym...@li...
> Subject: [PyMOL] Pymol script screenplay
>=20
>=20
> Hi List!
>=20
> I finally got a Pymol script which does what I want, but I still have
> problems.  I follows my actual script:
>=20
> -------------------------------------
> del all
> mclear
> set cache_frames=3D0
> 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=3D1
> viewport 640,480
> run Pymol/eixos.py
> translate [18,18,20],object=3Daxes
> run Pymol/cgotext.py
> translate [18,55.5,40],object=3Dtxt
> 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=3D1.0
> set ray_trace_frames=3D1
> mpng png2/mvc1e2
> -------------------------------------------
>=20
> 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.
>=20
> BTW, how could I insert in Pymol script (python language) such command
> bellow:
>=20
> mencoder \*.png -mf on:fps=3D30 -o mvc1ec2.avi -ovc lavc -lavcopts
> vcodec=3Dmpeg4:vbitrate=3D6000:vhq:keyint=3D30
>=20
>=20
> Thanks in advance for any help.
>=20
> Cheers,
>=20
> --
> --------------------------
> Alan Wilter Sousa da Silva
> --------------------------
> B.Sc. - Dep. F=EDsica - UFPA
> M.Sc. - Dep. F=EDsica - PUC/RJ
> D.Sc. - IBCCF/UFRJ
> Bolsista Pesquisador LAC-INPE
> S=E3o Jos=E9 dos Campos (SP), Brasil
> www.lac.inpe.br/~alan
>=20
>=20
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