pymol-users Mailing List for PyMOL Molecular Graphics System

Doug,

For now, render in command-line mode using a script to circumvent this
limitation with the viewport command.

pymol -qc your_script.pml

where your_script.pml has:

 	viewport 2560,1920
 	set ray_trace_images = 1
 	mpng movieimages

I'll see what I can do about getting around Window system limitations in
future versions...

Cheers,
Warren


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

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Douglas Freymann
> Sent: Thursday, April 29, 2004 2:02 PM
> To: pym...@li...
> Subject: [PyMOL] mpng resolution?
> 
> How do you set the resolution of the rendered frames for a movie?
> 
> With a single image I can use:
> 	ray 2560,1920;  png hiresimage.png
> and 'hiresimage.png' looks good...
> 
> I see that there's a viewport command, but...
> if I set viewport 2560,1920 then,
> 	viewport 2560,1920
> 	set ray_trace_images = 1
> 	mpng movieimages
> then, I get 'movieimages.png' images that are 2560x964 pixels 
> (on my system OS X,  using a
> 1600x1024 display), which just looks goofy.
> 
> Do I have other options here?
> 
> Thanks,
> 
> Doug
> 
> -- 
> 
> Douglas M. Freymann          fre...@no...
> 
> Molecular Pharmacology & Biological Chemistry Ward 7-247,  
> Northwestern University
> 303 E. Chicago Ave., Chicago, IL  60611
> 
> (312) 503-1877                    fax: (312) 503-5349
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: Oracle 10g Get certified 
> on the hottest thing ever to hit the market... Oracle 10g. 
> Take an Oracle 10g class now, and we'll give you the exam FREE.
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> _______________________________________________
> PyMOL-users mailing list
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> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

How do you set the resolution of the rendered frames for a movie?

With a single image I can use:
	ray 2560,1920;  png hiresimage.png
and 'hiresimage.png' looks good...

I see that there's a viewport command, but...
if I set viewport 2560,1920 then,
	viewport 2560,1920
	set ray_trace_images = 1
	mpng movieimages
then, I get 'movieimages.png' images that are 2560x964 pixels (on my 
system OS X,  using a
1600x1024 display), which just looks goofy.

Do I have other options here?

Thanks,

Doug

-- 

Douglas M. Freymann          fre...@no...

Molecular Pharmacology & Biological Chemistry
Ward 7-247,  Northwestern University
303 E. Chicago Ave., Chicago, IL  60611

(312) 503-1877                    fax: (312) 503-5349

Reece,

PyMOL already has full alpha support for transparency and backgrounds.

To get that floating effect in PowerPoint, Photoshop, or Keynote:

set ray_opaque_background, off
ray
png my_alpha_image.png

That's one of the reasons I like PNG format, but beware of using transparent
images in web pages:  Most current Windows versions of IE don't have alpha
channel support with PNG files (or any 32-bit image format AFAIK).

Cheers,
Warren


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

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Reece Hart
> Sent: Tuesday, April 27, 2004 8:54 PM
> To: pym...@li...
> Subject: Re: [PyMOL] True Black?
> 
> On Tue, 2004-04-27 at 17:27, pdo...@ch... wrote: 
> 
> 	Thanks for the suggestion. Unfortunately this still 
> gives me a very light 
> 	grey--nowhere near what you are seeing on your machine. 
> The molecule is 
> 	*clearly* visible against the black background. I am 
> using pymol on win XP. I 
> 	think I will put pymol on my linux machine and see if 
> that makes a difference.
> 
> 
> Pete-
> 
> I assume that what you're seeing is the result of minute 
> scattering during ray tracing (Warren- is this correct?). 
> That's just a guess.
> 
> Whatever the cause, you might consider using an image editor 
> like the gimp <" rel="nofollow">http://www.gimp.org/>  (see * below; or 
> Photoshop on Windows, I guess) to select all pixels within 
> some distance of black and recoloring those as exactly black. 
> For a neater effect, you could add an alpha channel and make 
> the pixels transparent, in which case your ray traced image 
> would appear to "float" on whatever background you used.
> 
> Come to think of it, perhaps this would make a useful setting 
> in PyMOL itself (unless it already exists and I just haven't 
> come across it): a flatten_background setting (a rgb 
> distance) which would cause any pixel within the that 
> distance of the background color to be set exactly to the 
> background color. If background color were extended to 
> include an alpha channel, then this idea would also provide 
> for transparent backgrounds.
> 
> -Reece
> 
> * If you're using gimp, do this: load the png, add an alpha 
> channel (Image > Alpha > Add Alpha Channel), then select by 
> color (Select > By Color..., then click black somewhere), 
> then either 1) fill with the bucket to set the color or 2) 
> cut the selection to make it transparent. 
> 
> 
> 
> 
> -- 
> Reece Hart, Ph.D.                       rk...@ge..., 
> http://www.gene.com/
> Genentech, Inc.                         650-225-6133 (voice), 
> -5389 (fax)
> Bioinformatics and Protein Engineering
> 1 DNA Way, MS-93                        
> http://www.in-machina.com/~reece/
> South San Francisco, CA  94080-4990     re...@in..., 
> GPG: 0x25EC91A0
> <" rel="nofollow">http://www.gimp.org/> 
> 

On Tue, 2004-04-27 at 17:27, pdo...@ch... wrote:

> Thanks for the suggestion. Unfortunately this still gives me a very light 
> grey--nowhere near what you are seeing on your machine. The molecule is 
> *clearly* visible against the black background. I am using pymol on win XP. I 
> think I will put pymol on my linux machine and see if that makes a difference.


Pete-

I assume that what you're seeing is the result of minute scattering
during ray tracing (Warren- is this correct?). That's just a guess.

Whatever the cause, you might consider using an image editor like the
gimp (see * below; or Photoshop on Windows, I guess) to select all
pixels within some distance of black and recoloring those as exactly
black. For a neater effect, you could add an alpha channel and make the
pixels transparent, in which case your ray traced image would appear to
"float" on whatever background you used.

Come to think of it, perhaps this would make a useful setting in PyMOL
itself (unless it already exists and I just haven't come across it): a
flatten_background setting (a rgb distance) which would cause any pixel
within the that distance of the background color to be set exactly to
the background color. If background color were extended to include an
alpha channel, then this idea would also provide for transparent
backgrounds.

-Reece

* If you're using gimp, do this: load the png, add an alpha channel
(Image > Alpha > Add Alpha Channel), then select by color (Select > By
Color..., then click black somewhere), then either 1) fill with the
bucket to set the color or 2) cut the selection to make it transparent.

-- 
Reece Hart, Ph.D.                       rk...@ge..., http://www.gene.com/
Genentech, Inc.                         650-225-6133 (voice), -5389 (fax)
Bioinformatics and Protein Engineering
1 DNA Way, MS-93                        http://www.in-machina.com/~reece/
South San Francisco, CA  94080-4990     re...@in..., GPG: 0x25EC91A0

Hi,

> I've playing around once with nice movies but memory has been a problem. =
> =20
> Now I got a dual Athlon with 2Mb Ram, but didn't test it yet, I'm afraid=20
> (such server cannot stop :-).

My Dual Opteron has been rendering our scene 4 for 19 hours now. (!! &
:( ).  Scenes 1 and 2 take something like 1-2 hours total.  Scene 4's a
bit more complex.

> I'm wondering if (and that's my suggestion to you Jason) it'd be a nice=20
> idea parting you movie in several takes (as I did for the example above),=
> =20
> like "playing-as-a-director-in-a-real-movie".

This is actually what we did.  We created 4 scenes ideas and scripted
them.  We then did something like 'viewport 20, 20' and commented out
the mpng commands.  Next we played the movies through (quickly; no
rendering) and saved state(s).  So, we distributed the render process
over 3 machines.  Unfortunaly my laptop's not even strong enough to LOAD
the scenes (~100,000 atoms+movie+stored scenes) let alone render them! 
(Intel P4 w/512 MB RAM!)

Waiting my this machine render is like watching grass grow.  :(  I'm now
relegated to a simple P4 and old 1 GHz server while it renders.  :(  I'm
not even sure this task would have been tangible 3-5 years ago.

Thanks for the suggestion!

Regards,

-- Jason

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

Wow! That's it. I wonder why that works but setting the rbg for "black" to 
0,0,0 doesn't?

I used:

set_color new_black, [0,0,0]

select all

color new_black


Looks mahvelous.
Thanks a lot.

Pete
UCLA Chemistry


Thomas Stout <ts...@ex...> said:

> 
> I have defined a new color in PyMOL that gets me closer to "real" black:
> 
> pymol> set_color new_black [0,0,0]
> 
> then,
> 
> pymol> color new_black obj01
> 
> It's not really, completely total black, but it's much blacker than 
> whatever Warren has defined in the pull-down menu!
> 
> -Tom
> 
> 
> >Hello Matt,
> >
> >Thanks for the suggestion. Unfortunately this still gives me a very light
> >grey--nowhere near what you are seeing on your machine. The molecule is
> >*clearly* visible against the black background. I am using pymol on win 
XP. I
> >think I will put pymol on my linux machine and see if that makes a 
difference.
> >
> >Pete
> >
> >
> >Matt Franklin <fra...@ge...> said:
> >
> >>
> >>  On Monday, April 26, 2004, at 04:19  PM, <pdo...@ch...> wrote:
> >>
> >>  > Hello Pymoliacs,
> >>  >
> >>  > I have been playing around with the lighting and gamma settings, but
> >>  > can
> >>  > never get a true black. The black always shows up as grey. Does anyone
> >>  > know
> >>  > how to get black to be black?
> >>  >
> >>  > Pete D.
> >>  > UCLA Chemistry
> >>  >
> >>  >
> >>
> >>  Hi Pete -
> >>
> >>  If what you want is a "flat black", i.e. just a silhouette of the
> >>  ribbon/surface/whatever, then set the color to black and turn the
> >>  specular reflections off ("set specular, 0").  This certainly looks
> >>  like rgb 0,0,0 to me (MacPymol v.0.94, OS X 10.2.8) and is completely
> >>  invisible in front of a black background.  If you're looking for a
> >>  black with some texture visible, then you will get some gr(e/a)y in
> >>  with your black...
> >>
> >>  Hope this helps,
> >>
> >>  Matt
> >>
> >>  --
> >>  Matthew Franklin            Phone:(650)225-4596
> >>  Postdoctoral Researcher       Fax:(650)225-3734
> >>  Genentech, Inc.
> >>  1 DNA Way, South San Francisco, CA 94080
> >>
> >
> >
> >
> >--
> >
> >
> >
> >
> >
> >-------------------------------------------------------
> >This SF.Net email is sponsored by: Oracle 10g
> >Get certified on the hottest thing ever to hit the market... Oracle 10g.
> >Take an Oracle 10g class now, and we'll give you the exam FREE.
> >http://ads.osdn.com/?ad_id=3149&alloc_id=8166&op=click
> >_______________________________________________
> >PyMOL-users mailing list
> >PyM...@li...
> >https://lists.sourceforge.net/lists/listinfo/pymol-users
> 



-- 

Hello Matt,

Thanks for the suggestion. Unfortunately this still gives me a very light 
grey--nowhere near what you are seeing on your machine. The molecule is 
*clearly* visible against the black background. I am using pymol on win XP. I 
think I will put pymol on my linux machine and see if that makes a difference.

Pete


Matt Franklin <fra...@ge...> said:

> 
> On Monday, April 26, 2004, at 04:19  PM, <pdo...@ch...> wrote:
> 
> > Hello Pymoliacs,
> >
> > I have been playing around with the lighting and gamma settings, but 
> > can
> > never get a true black. The black always shows up as grey. Does anyone 
> > know
> > how to get black to be black?
> >
> > Pete D.
> > UCLA Chemistry
> >
> >
> 
> Hi Pete -
> 
> If what you want is a "flat black", i.e. just a silhouette of the 
> ribbon/surface/whatever, then set the color to black and turn the 
> specular reflections off ("set specular, 0").  This certainly looks 
> like rgb 0,0,0 to me (MacPymol v.0.94, OS X 10.2.8) and is completely 
> invisible in front of a black background.  If you're looking for a 
> black with some texture visible, then you will get some gr(e/a)y in 
> with your black...
> 
> Hope this helps,
> 
> Matt
> 
> -- 
> Matthew Franklin            Phone:(650)225-4596
> Postdoctoral Researcher       Fax:(650)225-3734
> Genentech, Inc.
> 1 DNA Way, South San Francisco, CA 94080
> 



-- 

Hi Warren and Jason.

I've playing around once with nice movies but memory has been a problem. =
=20
Now I got a dual Athlon with 2Mb Ram, but didn't test it yet, I'm afraid=20
(such server cannot stop :-).

Warren, you really have a great software and I really want to do with it=20
what I've done with VMD.  See an example:
http://www.lac.inpe.br/~alan/IntroducingMD.avi

I'm wondering if (and that's my suggestion to you Jason) it'd be a nice=20
idea parting you movie in several takes (as I did for the example above),=
=20
like "playing-as-a-director-in-a-real-movie".

When I get a spare time I'll try to get back to my movies.

Cheers,
Alan

On Sun, 25 Apr 2004 pym...@li... wrote:

> Today's Topics:
>=20
>    1. Does (PDB) size really matter? (Jason Vertrees)
>=20
> Warren,
>=20
> Thanks!  I was setting 'hash_max' higher and higher (but my memory
> monitor always showed at least 90 megs free at the least).  I'll try the
> lower hash_max; I'll try lower this time.
>=20
> I think we have a really great movie in the works, and as I play with
> PyMol more and more, I can make much cooler things.  You've got some
> great software here!
>=20
> My 0.96b2 PSE file is bzipped, for all to download, at
> http://www.vertrees.org/~tree/scene1.pse.bz2 it's about 2.7 MB; The 0.95
> PSE file is http://www.vertrees.org/~tree/095_scene1.pse.bz2.=20
> atom_count is about 85,000 for them. =20
>=20
> The movie script is as in the previous message. =20
>=20
> As of now, I'll try smaller hash_max's and also if that's not good,
> reduce the size of my circular lipid bilayer.
>=20
> Many thanks for the quick response!
>=20
> Regards,
>=20
> -- Jason
>=20

--=20
--------------------------
Alan Wilter Sousa da Silva
--------------------------
D.Sc. - IBCCF/UFRJ
Bolsista Pesquisador LAC-INPE
S=E3o Jos=E9 dos Campos (SP), Brasil
www.lac.inpe.br/~alan

Dear all,

we just considering to purchase new linux pcs and i would be very intereste=
d=20
in the latest hardware recommendations?

we are planning to use these machines for stereo visualization with pymol a=
nd=20
O.

cheers,


peter


ps. has the pymol Xig Summit2.2 problem been resolved?
=2D-=20
 ___________________________________________

Dr. Peter Haebel

Philipps-Universit=E4t Marburg
Institut f=FCr Pharmazeutische Chemie
Marbacher Weg 6
D-35032 Marburg

phone: +49-6421-28-25072
fax: +49-6421-28-28994

email: pet...@st...
http://www.agklebe.de

On Monday, April 26, 2004, at 04:19  PM, <pdo...@ch...> wrote:

> Hello Pymoliacs,
>
> I have been playing around with the lighting and gamma settings, but 
> can
> never get a true black. The black always shows up as grey. Does anyone 
> know
> how to get black to be black?
>
> Pete D.
> UCLA Chemistry
>
>

Hi Pete -

If what you want is a "flat black", i.e. just a silhouette of the 
ribbon/surface/whatever, then set the color to black and turn the 
specular reflections off ("set specular, 0").  This certainly looks 
like rgb 0,0,0 to me (MacPymol v.0.94, OS X 10.2.8) and is completely 
invisible in front of a black background.  If you're looking for a 
black with some texture visible, then you will get some gr(e/a)y in 
with your black...

Hope this helps,

Matt

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

Hello Pymoliacs,

I have been playing around with the lighting and gamma settings, but can 
never get a true black. The black always shows up as grey. Does anyone know 
how to get black to be black?

Pete D.
UCLA Chemistry

Hi Jason,

I see you have hash_max set to 400 -- that's the problem. 

In empirical testing, I found that there is rarely a reason to go above 200
with this setting.  Having a hash table that is too finely sampled is no
better than having one too coarsely sampled.  PyMOL's default of 100 is
intended to avoid running out of RAM on systems with just 256 MB.  If you
have more RAM, then going up to 150 or 170 is usually worth it.  250 may
sometimes be helpful, but 400 is almost certainly overkill.  Because this is
a 3D hash table, each 2X increase can potentially involve an 8X increase in
memory required.

set hash_max,200
set antialias,1
produces the following image in 204 seconds using 948 MB of RAM on a dual G5

http://delsci.com/img/scene1.jpg

with "set light, [-0.4,0.4,-1]":

http://delsci.com/img/scene1_flip_light.jpg

You can mellow out that techno-green and give your scene a more natural feel
with:

set ray_blend_green, 0.4
set ray_blend_colors, on

http://delsci.com/img/scene1_mellow.jpg

And then, it helps to back off on the green color itself, so that those
spheres don't look so over-lit:

set_color green, [0.25,0.75,0.25]
rebuild

Now you've got a reasonably balanced image...

http://delsci.com/img/scene1_final.jpg

Cheers,
Warren

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Jason Vertrees
> Sent: Saturday, April 24, 2004 11:03 PM
> To: PyMol Users List
> Subject: [PyMOL] Does (PDB) size really matter?
> 
> Warren,
> 
> Thanks!  I was setting 'hash_max' higher and higher (but my 
> memory monitor always showed at least 90 megs free at the 
> least).  I'll try the lower hash_max; I'll try lower this time.
> 
> I think we have a really great movie in the works, and as I 
> play with PyMol more and more, I can make much cooler things. 
>  You've got some great software here!
> 
> My 0.96b2 PSE file is bzipped, for all to download, at
> http://www.vertrees.org/~tree/scene1.pse.bz2 it's about 2.7 
> MB; The 0.95 PSE file is 
> http://www.vertrees.org/~tree/095_scene1.pse.bz2. 
> atom_count is about 85,000 for them.  
> 
> The movie script is as in the previous message.  
> 
> As of now, I'll try smaller hash_max's and also if that's not 
> good, reduce the size of my circular lipid bilayer.
> 
> Many thanks for the quick response!
> 
> Regards,
> 
> -- Jason
> 
> 
> --
> Jason Vertrees
> BSCB Graduate Student @ UTMB, Galveston
> jav...@ut... :: http://www.bscb.utmb.edu
> 
> 
> -------------------------------------------------------
> This SF.net email is sponsored by: The Robotic Monkeys at ThinkGeek
> For a limited time only, get FREE Ground shipping on all orders of $35
> or more. Hurry up and shop folks, this offer expires April 30th!
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> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

Hello!
I have 2 questions:
1) What is the correct/common email address to send your questions on PyMOL?
2) I have downloaded PyMOL on a PC(microsoft windows XP)using the instructions posted on the PyMOL site. But I am not able to get input files form the Internet--I simply wanted to go to the PUBMED and get the structure of a protein from PUBMED/web directly into the PyMOL. SO going to the external GUI of PyMOL , then File, then Open did not give me the option of opening the internet eventhough it is on our desktop. I could open other files such as :my computer, my files, my network places, just not the Internet!!! Does anybody know how to do it?
Thank you for your time and consideration,
ELham

PyMolers,

I've got my final scenes laid out, but when I rendered the move frames I
got some weirdness in the final screens.  The weirdness is that we have
a gray background and have some spheres and sticks fade out; however,
when they fade they don't go transparent - they go to a different color
of gray and when rotated into the movie -- it doesn't look so hot.

Any ideas on how to turn this off?


PyMol 0.95 PSE : http://vertrees.org/~tree/095_new_scene1.pse.tgz
Movie script #1: http://vertrees.org/~tree/bad_scene1.py
Sample render  : http://vertrees.org/~tree/scene2_0013.png

In the sample png above, I would like the light grey regions to be
transparent.  It also seems as if the quality of the render has gotten
much poorer.  Any ideas?

-- Jason

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

Warren,

Thanks!  I was setting 'hash_max' higher and higher (but my memory
monitor always showed at least 90 megs free at the least).  I'll try the
lower hash_max; I'll try lower this time.

I think we have a really great movie in the works, and as I play with
PyMol more and more, I can make much cooler things.  You've got some
great software here!

My 0.96b2 PSE file is bzipped, for all to download, at
http://www.vertrees.org/~tree/scene1.pse.bz2 it's about 2.7 MB; The 0.95
PSE file is http://www.vertrees.org/~tree/095_scene1.pse.bz2. 
atom_count is about 85,000 for them.  

The movie script is as in the previous message.  

As of now, I'll try smaller hash_max's and also if that's not good,
reduce the size of my circular lipid bilayer.

Many thanks for the quick response!

Regards,

-- Jason


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

Ack!  Sorry to hear this.

The two things that determine memory usage when rendering are:

1) the total number of primitives (spheres, triangles, cylinder [i.e. lines]
etc.)
2) the value of hash_max

#1 may not be easily remedied for your scene

#2 can be improved by setting hash_max to something like 65 or 50.
Rendering will take much longer, but less RAM will be used.

~200k atoms really shouldn't be a problem on a machine with that kind of
RAM, so there is also a chance here you might be experiencing a bug.  It
might be worth emailing me a (compressed?) copy of the session file just to
be sure...

I don't see anything wrong with your script.

Cheers,
Warren

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Jason Vertrees
> Sent: Saturday, April 24, 2004 6:50 PM
> To: PyMol Users List
> Cc: Tzintzuni Garcia I.; Roger B. Sutton
> Subject: [PyMOL] Does (PDB) size really matter? (Help!)
> 
> PyMolers,
> 
> Our setup is a Dual Xeon 3.2 GHz 1GB RAM and Nvidia Quadro 
> running PyMol 0.95.  (Also available, Dual Opteron 240 64-Bit 
> Linux w/0.95 w/1 GB RAM w/same problems.)
> 
> We are trying to render a nifty movie but can't.  PyMol keeps 
> crashing during the render process.  The scene had originally 
> 185,000 atoms, but now I've snipped out some cutting it down 
> to 85,000 or so.
> 
> The command "ray 800, 600" dies.  I then collected all of my 
> bilayer segment objects into one larger one (so, instead of 8 
> objects I had one 8x as large, hoping that the reduction in 
> the number of objects freed up some RAM.)
> 
> The movie script for scene1 is 
> http://www.vertrees.org/~tree/scene1.py. 
> I'm very new to making movies, but it does what I want.
> 
> Here's some PyMol output:
> 
> PyMOL>count_atoms
>  count_atoms: 86220 atoms
> 
> PyMOL>ray
> VLAMalloc-ERR: realloc failed
> **************************************************************
> **************
> *** EEK!  PyMOL just ran out of memory and crashed.  To get 
> around this,
> ***
> *** you may need to reduce the quality, size, or complexity 
> of the scene
> ***
> *** that you are viewing or rendering.    Sorry for the 
> inconvenience...
> ***
> **************************************************************
> **************
> /usr/bin/pymol.com: line 2: 11531 Aborted                
> /usr/bin/python 
> /usr/lib64/python2.3/site-packages/pymol/__init__.py $*
> 
> Any ideas on how we can keep the movie w/o sacrificing 
> quality or number of atoms?  If need be, I can probably trim 
> another 3,000-10,000 (max) atoms out.
> 
> 
> Much TIA,
> 
> -- Jason
> 
> --
> Jason Vertrees
> BSCB Graduate Student @ UTMB, Galveston
> jav...@ut... :: http://www.bscb.utmb.edu
> 
> 
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PyMolers,

Our setup is a Dual Xeon 3.2 GHz 1GB RAM and Nvidia Quadro running PyMol
0.95.  (Also available, Dual Opteron 240 64-Bit Linux w/0.95 w/1 GB RAM
w/same problems.)

We are trying to render a nifty movie but can't.  PyMol keeps crashing
during the render process.  The scene had originally 185,000 atoms, but
now I've snipped out some cutting it down to 85,000 or so.

The command "ray 800, 600" dies.  I then collected all of my bilayer
segment objects into one larger one (so, instead of 8 objects I had one
8x as large, hoping that the reduction in the number of objects freed up
some RAM.)

The movie script for scene1 is http://www.vertrees.org/~tree/scene1.py. 
I'm very new to making movies, but it does what I want.

Here's some PyMol output:

PyMOL>count_atoms
 count_atoms: 86220 atoms

PyMOL>ray
VLAMalloc-ERR: realloc failed
****************************************************************************
*** EEK!  PyMOL just ran out of memory and crashed.  To get around this,
***
*** you may need to reduce the quality, size, or complexity of the scene
***
*** that you are viewing or rendering.    Sorry for the inconvenience...
***
****************************************************************************
/usr/bin/pymol.com: line 2: 11531 Aborted                
/usr/bin/python /usr/lib64/python2.3/site-packages/pymol/__init__.py $*

Any ideas on how we can keep the movie w/o sacrificing quality or number
of atoms?  If need be, I can probably trim another 3,000-10,000 (max)
atoms out.


Much TIA,

-- Jason

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

Howdy,

I've started writing some more intricate scripts for a movie my prof's
doing _very_ soon.

I have PyMol 0.95 on either a Dual Xeon 3.4 or a Dual Opteron 240 64-Bit
both running Linux 2.6.5.  Using 'mencoder' to encode movies.

We've made great progress but would like to mimic a photon by using a
small light source (small CGO sphere?) smashing into a rhodopsin to
activate it.  Does PyMol restrict us to only have light sources behind
the camera/view?  Can I simulate this with CGO's or does PyMol have
something better built in (that my Google searches failed to find)?

Next, does rTools work for 0.95?  Right now I'm hand making movies
(which is perfectly fine), but I hear that rTools offers some very nifty
features.

Lastly, thanks again to Warren et. al. for such cool software; not only
great for visualization but teaching and thinking about biology as well.

TIA,

-- Jason

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

Daqi,

Not sure if this is exactly what you're asking, but, as of v0.88, alter 
the "cartoon_highlight_color" setting to get Molscript-like effects.  
For example:

> set cartoon_highlight_color, grey70

See "http://chips.csb.ki.se/pymol/msg01017.html" for more info.

   Cameron



=== da...@ma... wrote (on 04/22/2004 12:03 AM): ===

>Hi, all:
>
>I just picked up pymol tonight and found it quite impressive.
>
>Does anyone know how to color one side of a molecular surface with one color 
>and the other side with a different color?  Thanks in advance.
>
>daqi
>
>
>
>
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-- 
Cameron Mura
UCSD

Christian,

	This isn't implemented yet, but it is on the to do list.

Cheers,
Warren
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Christian Rummey
> Sent: Thursday, April 22, 2004 2:35 AM
> To: pym...@li...
> Subject: [PyMOL] (no subject)
> 
> 
> hi ppl,
> 
> is there a way to sort the list of objects/selections in the 
> panel on the right side other than loading/selecting stuff in 
> a specific order?
> 
> simple example: I compare several ligands in a specific site, 
> and save the data as pymol sessions; after adding new 
> ligands//site conformations I'd like to sort the sites 1st, 
> then the ligands. 
> 
> any hints?
> 
> thanks a lot,
> christian
> 
> --
> NEU : GMX Internet.FreeDSL
> Ab sofort DSL-Tarif ohne Grundgeb|hr: http://www.gmx.net/dsl
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials
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> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

hi ppl,

is there a way to sort the list of objects/selections in the panel on the
right side other than loading/selecting stuff in a specific order?

simple example: I compare several ligands in a specific site, and save the
data as pymol sessions; after adding new ligands//site conformations I'd
like to sort the sites 1st, then the ligands. 

any hints?

thanks a lot,
christian

-- 
NEU : GMX Internet.FreeDSL
Ab sofort DSL-Tarif ohne Grundgebühr: http://www.gmx.net/dsl

Hi, all:

I just picked up pymol tonight and found it quite impressive.

Does anyone know how to color one side of a molecular surface with one color 
and the other side with a different color?  Thanks in advance.

daqi

Mark,

	The sphere_scale setting is a multiplier of the atom's VDW radius.
If you want to set exact radii, use "alter":

alter selection, vdw=number

eg.  alter (all), vdw=1.0
     rebuild

Cheers,
Warren
 


> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Mark Del Campo
> Sent: Wednesday, April 21, 2004 3:40 PM
> To: pym...@li...
> Subject: [PyMOL] sphere scale
> 
> 
> Anybody know the precise size in angstroms corresponding to a 
> given sphere scale?
> 
> For instance, does a sphere_scale of 1.0 equal a radius of 
> 1.0 angstrom?
> 
> Thanks in advance!!
> 
> Mark Del Campo
> Univ. of Miami
> Malhotra lab
> 
> 
> 	
> 		
> __________________________________
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> 
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> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

Mark,

	The sphere_scale setting is a multiplier of the atom's VDW radius.
If you want to set exact radii, use "alter":

alter selection, vdw=number

eg.  alter (all), vdw=1.0
     rebuild

Cheers,
Warren
 


> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Mark Del Campo
> Sent: Wednesday, April 21, 2004 3:40 PM
> To: pym...@li...
> Subject: [PyMOL] sphere scale
> 
> 
> Anybody know the precise size in angstroms corresponding to a 
> given sphere scale?
> 
> For instance, does a sphere_scale of 1.0 equal a radius of 
> 1.0 angstrom?
> 
> Thanks in advance!!
> 
> Mark Del Campo
> Univ. of Miami
> Malhotra lab
> 
> 
> 	
> 		
> __________________________________
> Do you Yahoo!?
> Yahoo! Photos: High-quality 4x6 digital prints for 25"
> http://photos.yahoo.com/ph/print_splash
> 
> 
> -------------------------------------------------------
> 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=1470&alloc_id=3638&op=click
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

Hi, all:

I just picked up pymol tonight and found it quite impressive.

Does anyone know how to color one side of a molecular surface with one color and 
the other side with a different color?  Thanks in advance.

daqi