pymol-users Mailing List for PyMOL Molecular Graphics System

Hari,

isolevel mesh-name, level

Cheers,
Warren

________________________________________
From: hari jayaram [mailto:ha...@gm...] 
Sent: Wednesday, May 27, 2009 12:29 PM
To: pym...@li...
Subject: [PyMOL] update mesh level to custom value after deleting map object

H
I have an old pymol session file .
I have a mesh object displayed whose level I can manipulate in predetermined ways using the Action-Level-menu. I however want to pick a level different from the menu options provided . 

A further complication is that I have deleted the original map object and want to avoid going looking for it.

Is there a way to pick a level for a mesh object that is not pre-programmed into the Action menu .

Thanks 
Hari


 

On 15:02 Tue 26 May     , David Hall wrote:
> 
> is it possible to put a link to these archives in the signature 
> portion of the mailing list?  I would find that very helpful.

FYI, it's also in the headers of every list email:

List-Archive: <" rel="nofollow">http://sourceforge.net/mailarchive/forum.php?forum_name=pymol-users>

-- 
Thanks,
Donnie

Donnie Berkholz
P. Andrew Karplus lab
Oregon State University

H
I have an old pymol session file .
I have a mesh object displayed whose level I can manipulate in predetermined
ways using the Action-Level-menu. I however want to pick a level different
from the menu options provided .

A further complication is that I have deleted the original map object and
want to avoid going looking for it.

Is there a way to pick a level for a mesh object that is not pre-programmed
into the Action menu .

Thanks
Hari

set surface_mode, 1

Cheers,
Warren

> -----Original Message-----
> From: chaix denis [mailto:ch...@cb...]
> Sent: Tuesday, May 26, 2009 3:55 PM
> To: pym...@li...
> Cc: Chaix Denis; support; pym...@li...
> Subject: [PyMOL] surface of ligand
> 
> Dear users
> 
>     How can I obtain the surface of a ligand in protein pdb file.
>     I just need the simple surface, i doesn't need in this case, the
>     electrostatic surface.
>     Thanks
> 

Dear users

    How can I obtain the surface of a ligand in protein pdb file.
    I just need the simple surface, i doesn't need in this case, the
    electrostatic surface.
    Thanks



-- 
CHAIX Denis
PHD student
Centre de Biochimie Structurale
INSERM U554/CNRS 5048
29 rue de Navacelles
F-34090 Montpellier, France
Tel: 33 4 67 41 77 21
Fax: 33 4 67 41 79 13
e-mail:Den...@cb...
http://www.cbs.cnrs.fr

Hmm... let's see if this works!

> -----Original Message-----
> From: David Hall [mailto:dwa...@ya...]
> Sent: Tuesday, May 26, 2009 3:07 PM
> To: Warren DeLano; pymol-users
> Subject: Re: [PyMOL] The List Archive is Back!
> 
> 
> is it possible to put a link to these archives in the signature
portion of
> the mailing list?  I would find that very helpful.
> 
> -David

is it possible to put a link to these archives in the signature portion of the mailing list?  I would find that very helpful.

-David



----- Original Message ----
> From: Warren DeLano <wa...@de...>
> To: pymol-users <pym...@li...>
> Sent: Tuesday, April 28, 2009 11:52:28 PM
> Subject: [PyMOL] The List Archive is Back!
> 
> Folks,
> 
> Thanks to mail-archive.com, the PyMOL-Users list is now once again
> searchable:
> 
> http://www.mail-archive.com/pym...@li...
> 
> The new search syntax is summarized at:
> 
> http://www.mail-archive.com/faq.html#search
> 
> For example, you can now quickly identify all 22 posts which have
> discussed "surface area":
> 
> http://www.mail-archive.com/search?l=p...@li...&q
> =%22surface+area%22
> 
> Or you can check out Tsjerk's ~170+ helpful contributions to the list
> over the past six years:
> 
> http://www.mail-archive.com/search?l=p...@li...&q
> =from%3AWassenaar
> 
> Please everyone get in the habit of consulting this archive before
> posting questions which may have the potential for being
> frequently-asked.  There are nearly 7,000 posts at your beck and call.
> 
> Cheers,
> Warren
> 
> 
> ------------------------------------------------------------------------------
> Register Now & Save for Velocity, the Web Performance & Operations 
> Conference from O'Reilly Media. Velocity features a full day of 
> expert-led, hands-on workshops and two days of sessions from industry 
> leaders in dedicated Performance & Operations tracks. Use code vel09scf 
> and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users



      

Sean, 
 
You can save some time & a lot of memory by loading the file and
removing the atoms in a single-line compound statement (with a semicolon
after the load statement).
 
load 1E3M.pdb; remove not A-C+F//

Cheers,
Warren
 

________________________________

	From: Sean Law [mailto:mag...@ho...] 
	Sent: Tuesday, May 26, 2009 9:10 AM
	To: pym...@li...
	Subject: [PyMOL] Load Selection
	
	
	Hi PyMOLers,
	
	I was wondering if there is a way to load part of a PDB file if
you know a priori what you want thereby saving time/memory?
	
	Currently, I have a system that is ~160,000 atoms (protein-DNA
complex with explicit water molecules taken from an MD simulation).
When I load more than 10 structures I start running out of memory so I
was hoping that there was some way that I could specify on the command
line to only load the protein/DNA but not the water.  Right now, I have
to pre-process each pdb file before loading which seems tedious.  I was
hoping that there was already some built-in function in PyMOL that can
handle this immediately by invoking something like:
	
	load 1E3M.pdb, selection="c. a+b or c. e+f"
	
	Thank you for your time.
	
	Sean
	
	
________________________________

	Create a cool, new character for your Windows Live(tm)
Messenger. Check it out <" rel="nofollow">http://go.microsoft.com/?linkid=9656621>  

Hi PyMOLers,

I was wondering if there is a way to load part of a PDB file if you know a priori what you want thereby saving time/memory?

Currently, I have a system that is ~160,000 atoms (protein-DNA complex with explicit water molecules taken from an MD simulation).  When I load more than 10 structures I start running out of memory so I was hoping that there was some way that I could specify on the command line to only load the protein/DNA but not the water.  Right now, I have to pre-process each pdb file before loading which seems tedious.  I was hoping that there was already some built-in function in PyMOL that can handle this immediately by invoking something like:

load 1E3M.pdb, selection="c. a+b or c. e+f"

Thank you for your time.

Sean

_________________________________________________________________
Create a cool, new character for your Windows Live™ Messenger. 
http://go.microsoft.com/?linkid=9656621

    I'm trying to examine electrostatics for an RNA molecule.  I've 
calculated an electrostatics map using Qnifft (which outputs the map as 
a .phi file).  I can read the .phi file into PyMol and color my 
molecular surface using the map.  What I'm hoping to do is 
quantitatively determine the potential at a given spot on the surface.  
In Spock (http://quorum.tamu.edu/) , I can click on a spot on the 
surface and it will print out a the potential at that spot.  Is there 
any similar ability within PyMol?  Alternatively, is there any way to 
determine the surface potential for a specified atom?  I'm hoping to do 
this in PyMol because Spock can only read in maps up to 129x129x129 
units in size, and PyMol seems to handle the largest maps that Qnifft 
can generate.  I did a search through the list archives and found a few 
questions that related to electrostatics, but didn't find anything to 
help me with this issue.

    Thanks in advance,
    Kevin Keating
    Pyle lab, Yale University

Hello!
I save the surface of a protein as a .wrl, then I calculate 
the electrostatic potential and I save again the surface of 
the protein. I import the two surfaces in Blender (a 3D 
software) and I see that they are shifted. Why does this 
happen? Then I open the .wrl files and the .dx file in another 
home made program and I see that the surfaces and the grid 
have not the same origin. Can somebody tell me why the surface 
and the grid don't have the same origin and what do I have to 
do in order to fix this? I use pyMOL 1.1eval and APBS 1.0.0.

Thank you,
Raluca

Hello!
I save the surface of a protein as a .wrl, then I calculate 
the electrostatic potential and I save again the surface of 
the protein. I import the two surfaces in Blender (a 3D 
software) and I see that they are shifted. Why does this 
happen? Then I open the .wrl files and the .dx file in another 
home made program and I see that the surfaces and the grid 
have not the same origin. Can somebody tell me why the surface 
and the grid don't have the same origin and what do I have to 
do in order to fix this?

Thank you,
Raluca

Folks,

 

For quite some time now, we have ourselves experienced and continued to
receive complaints regarding graphics artifacts and other glitches with
ATI/AMD Radeon "HD" graphics chips on multiple platforms.  Though we
haven't had time to investigate everything to our satisfaction, it is
worth noting that such issues are conspicuously absent from those using
recent nVidia and Intel graphics chips, and that they also do not occur
with older ATI chips -- only the newer "HD" -branded models.

 

Therefore, if you are given a choice with a new purchase today, we
strongly recommend going with nVidia-based graphics chips for running
PyMOL.  Intel chips work fine too though they aren't typically as fast.

 

Just to be clear, we don't know for certain yet whether the fault lies
with PyMOL, with the OpenGL drivers, or with the ATI graphics chips
themselves. but if you simply buy nVidia, then you can entirely avoid
having to deal with AMD/ATI-specific OpenGL problems.  Eventually these
problems will likely be worked out - the chips are just glitchy, not DOA
- but there is a lot to be said for deliberately avoiding problematic
scenarios altogether.

 

Cheers,

Warren

 

 

 

Jean,

 

Assuming that you are using the most recent PyMOL 1.2 beta build, first
create a Scene for each display you wish to show.  

 

(To do that, show everything the way you want and then select "Append"
from the "Scene" menu.  Repeat the process for each view / color /
representation you wish to show.  You can PgUp / PgDown through defined
Scenes.)

 

Then, to create the movie, select "Program -> Scene Loop -> Y-Rock -> #
seconds each" from the "Movie" menu.

 

Now you can write out the movie as either a series of PNG files or an
MPEG file using "Save Movie As..." from the "File" menu.

 

Using scenes to create movies is a lot easier than messing around with
scripts : )!

 

Cheers,

Warren

 

________________________________

From: Jasinski, Jean Marie [mailto:Jea...@uc...] 
Sent: Tuesday, May 19, 2009 11:06 AM
To: pym...@li...
Subject: [PyMOL] Documentation and advice for external GUI Movies
commands?

 

My goal is to make a simple movie from PyMol for inclusion in a
powerpoint presentation.  I understand how to use the png files to make
an avi file.

 

What I need help with is using the external GUI Movie commands to make
my movie.  I want to use the x-rock command, turn on my ligand, x-rock
again, turn off ligand, display second ligand and repeat the process.
So far, I've only used the external GUI command line to do util.mrock. I
can't find documentation for the Movie commands (Program, Update
Program, etc.).  I figure I could use a script to do all the actions I
need, but I can't figure out how to call Movie/Program/Static
Loop/X-rock,.....

 

Thanks,

Jean Jasinski, Ph.D.

My goal is to make a simple movie from PyMol for inclusion in a powerpoint presentation.  I understand how to use the png files to make an avi file.

What I need help with is using the external GUI Movie commands to make my movie.  I want to use the x-rock command, turn on my ligand, x-rock again, turn off ligand, display second ligand and repeat the process.  So far, I've only used the external GUI command line to do util.mrock. I can't find documentation for the Movie commands (Program, Update Program, etc.).  I figure I could use a script to do all the actions I need, but I can't figure out how to call Movie/Program/Static Loop/X-rock,.....

Thanks,
Jean Jasinski, Ph.D.

Ah ha!  Yes, of course....

Many thanks to you & Rob for catching that!

Note to self: *triple* shots of espresso next time....   :)
-Tom

-----Original Message-----
From: Tsjerk Wassenaar [mailto:ts...@gm...] 
Sent: Saturday, May 16, 2009 1:30 AM
To: Thomas Stout
Cc: pymol-users
Subject: Re: [PyMOL] POVRAY Usage

Hi Tom,

Just as Robert says, the quote should be dropped. Maybe you should've had just one coffee more, but I should also have been more careful typing. Apparently I usually automatically start of with typing strings after .write( ;)

Sorry about that.

Tsjerk

On Fri, May 15, 2009 at 11:57 PM, Thomas Stout <ts...@ex...> wrote:
>
>
> Hi Tsjerk --
>
> What version of PyMOL does this work with?  I've been trying your 
> commands with versions 1.1 and 1.2b and while PyMOL reports that the 
> primitives have been processed, nothing is written to the file 
> "protein.pov" other than the header info:
>
>      camera {orthographic location <0.0 , 0.0 , 134.1048736572>
>      look_at  <0.0 , 0.0 , -1.0> right -74.9812240601*x up 
> 59.9849815369*y}
>      #default { finish{phong   -1.000 ambient    0.500 diffuse    
> 0.450 phong_size 13
>      .750000}}
>      light_source{<4000.0001,4000.0001,9865.8951>  rgb<1.0,1.0,1.0>}
>      plane{z , -206.0869
>       pigment{color rgb<1.0000,1.0000,1.0000>}
>       finish{phong 0 specular 0 diffuse 0 ambient 1.0}}
>      #include "povray.inc"
>
> and povray.inc contains:
>      cmd.get_povray()[1]
>
> If I save a povray file with the GUI menu selection: File> Save Image 
> As> POV-Ray then I get everything written to disk.  This occurs on 
> both linux and Windows.
>
> Am I missing something that would be more obvious if I had had more 
> coffee today?
>
> Thanks!
> -Tom
>
> PS - There was a missing quotation mark:
> open("povray.inc","w").write("cmd.get_povray()[1]) -->
> open("povray.inc","w").write("cmd.get_povray()[1]")
>
>
>
> -----Original Message-----
> From: Tsjerk Wassenaar [mailto:ts...@gm...]
> Sent: Thu 5/14/2009 1:47 PM
> To: Sean Law
> Cc: pymol-users
> Subject: Re: [PyMOL] POVRAY Usage
>
> Hi Sean,
>
> Unfortunately, getting a good image through POV-Ray requires editing 
> the POV-Ray file. You can write the scene to disk with the following 
> commands
>
> pov=open("protein.pov","w")
> pov.write(cmd.get_povray()[0])
> pov.write("#include \"povray.inc\"")
> pov.close()
>
> open("povray.inc","w").write("cmd.get_povray()[1])
>
> Then, take your favorite editor (under windows, you can use the 
> POV-Ray editor) and make some changes:
>
> 1. There's a line starting with #defaults. Remove that and replace it with:
>
> #default {
>     finish {
>         ambient .15
>         diffuse .5
>         specular 1
>         roughness .001
>         reflection { .5 metallic } // Remove this line for less 
> glossyness and faster tracing
>     }
> }
>
> 2. There's a light statement, which says:
> light_source{<4000.0001,4000.0001,9960.0000>  rgb<1.0,1.0,1.0>}.
> Replace it with:
>
> light_source
> {
>    <20,10,0>
>    rgb 2
>    area_light <5,5,0>,5,5
>    adaptive 1
>    jitter
> }
>
> This usually works for me :)
>
> Note that the trace may now take some time. Remove the metallic 
> reflection for faster tracing.
>
> I hope it helps. POV-Ray is cool, but rather complicated.
>
> Cheers,
>
> Tsjerk
>
> On Thu, May 14, 2009 at 10:21 PM, Sean Law <mag...@ho...> wrote:
>>
>> Hi All,
>>
>> While ray tracing a scene with 10 x-large proteins in grid mode at 
>> 3600, 3600 (width, height) I ran out of RAM (2 GB).  I tried it again 
>> by writing everything into a script and using pymol -qc which still ran out of memory.
>> I read somewhere that POVRAY is less of a memory hog so I installed 
>> the latest version and simply modified my script to "ray 3600, 3600, renderer=1"
>> to use POVRAY.  Everything went smoothly but I noticed that the image 
>> generated from POVRAY looked different than the native ray traced 
>> structure using PyMOL's ray tracer (simply invoking "ray" without 
>> dimensions in PyMOL).  Specifically, the light reflections appeared 
>> to be dulled in POVRAY and spheres that were further away from the 
>> camera view are not distinguishable.  I've posted a comparison on the PyMOLWiki:
>>
>> http://www.pymolwiki.org/index.php/Povray_vs._pymol
>>
>> Firstly, I apologize as I am completely new to the world of POVRAY 
>> and I just assumed that the image produced from either method would 
>> give identical/close results but I much prefer the look of the PyMOL ray-tracer.
>> Is there an easy way to set everything up the same way as the PyMOL 
>> ray-tracer but for POVRAY?  Thank you for your time.
>>
>> Sean
>>
>> ________________________________
>> Help keep personal info safe. Get Internet Explorer 8 today!
>>
>> ---------------------------------------------------------------------
>> --------- The NEW KODAK i700 Series Scanners deliver under ANY 
>> circumstances! Your production scanning environment may not be a 
>> perfect world - but thanks to Kodak, there's a perfect scanner to get 
>> the job done! With the NEW KODAK i700 Series Scanner you'll get full 
>> speed at 300 dpi even with all image processing features enabled. 
>> http://p.sf.net/sfu/kodak-com 
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>
> ----------------------------------------------------------------------
> -------- The NEW KODAK i700 Series Scanners deliver under ANY 
> circumstances! Your production scanning environment may not be a 
> perfect world - but thanks to Kodak, there's a perfect scanner to get 
> the job done! With the NEW KODAK i700 Series Scanner you'll get full 
> speed at 300 dpi even with all image processing features enabled. 
> http://p.sf.net/sfu/kodak-com 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
> This email (including any attachments) may contain material that is 
> confidential and privileged and is for the sole use of the intended 
> recipient. Any review, reliance or distribution by others or 
> forwarding without express permission is strictly prohibited. If you 
> are not the intended recipient, please contact the sender and delete 
> all copies.
> Exelixis, Inc. reserves the right, to the extent and under 
> circumstances permitted by applicable law, to retain, monitor and 
> intercept e-mail messages to and from its systems.
>
>



--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
This email (including any attachments) may contain material
that is confidential and privileged and is for the sole use of
the intended recipient. Any review, reliance or distribution by
others or forwarding without express permission is strictly
prohibited. If you are not the intended recipient, please
contact the sender and delete all copies.
Exelixis, Inc. reserves the right, to the extent and under
circumstances permitted by applicable law, to retain, monitor
and intercept e-mail messages to and from its systems.

Denis,

Sorry, PyMOL only has protein charges coded at present.  Perhaps the
APBS project's pdb2pqr utility might be able to assign charges to
canonoical ligands (such as ATP)?

http://apbs.sourceforge.net

Cheers,
Warren

> -----Original Message-----
> From: Chaix Denis [mailto:den...@cb...]
> Sent: Monday, May 18, 2009 9:10 AM
> To: pym...@li...
> Subject: [PyMOL] vacuum electrostatics
> 
> Dear users
> 
> I'm trying to compare the electrostatic charge surface of my protein
> with and without ligand, by using the command "generate vacuum
> electrostatics".
> that's works fine for the protein without ATP but that doesn't work
with
> the ligand.The surface obtaine doesn't take account the ligand
> 
> thanks
> 
> --
> CHAIX Denis
> 
> Centre de Biochimie Structurale
> INSERM U554/CNRS 5048
> 29 rue de Navacelles
> F-34090 Montpellier, France
> Tel: 33 4 67 41 77 21
> Fax: 33 4 67 41 79 13
> e-mail:Den...@cb...
> http://www.cbs.cnrs.fr
> 
> 
>
------------------------------------------------------------------------
--
> ----
> Crystal Reports - New Free Runtime and 30 Day Trial
> Check out the new simplified licensing option that enables
> unlimited royalty-free distribution of the report engine
> for externally facing server and web deployment.
> http://p.sf.net/sfu/businessobjects
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
> 
> 

Dear users

I'm trying to compare the electrostatic charge surface of my protein 
with and without ligand, by using the command "generate vacuum 
electrostatics".
that's works fine for the protein without ATP but that doesn't work with 
the ligand.The surface obtaine doesn't take account the ligand

thanks

-- 
CHAIX Denis

Centre de Biochimie Structurale 
INSERM U554/CNRS 5048 
29 rue de Navacelles 
F-34090 Montpellier, France 
Tel: 33 4 67 41 77 21
Fax: 33 4 67 41 79 13 
e-mail:Den...@cb...
http://www.cbs.cnrs.fr 

Hi Tsjerk!!,

 Yes,, it is really an oldie.. ( I tried to patch, but the new code is cpp
and not c anymore for povray, so I left the oldie goldie ). All I need is to
get close to pymol trace.. i.e. the shine which is missing in my links to
the pictures in my previous mail (this is just a very simple example i just
created to illustrate. But as the detail in a picture increases the effect
of ligting and shine also will change. Pymol's internal ray tracer nearly
always justice to these details, but as mentioned can have memory issues for
large pictures. So I need to go to povray to get my job done.  The settings
you suggested, I just used those blindly at the moment ( I will play with
those in the coming days).

 I wish I could write a povray file which by default does justice to the
picture generated. by povray when compared to internal ray tracer.

 thanks again for your help.
Abhi.

On Mon, May 18, 2009 at 4:58 PM, Tsjerk Wassenaar <ts...@gm...> wrote:

> Hi Abhi,
>
> Oooh, that's an oldie alright. I only vaguely recollect that coming in
> :) But you need to patch POV-Ray for it... Anyway, the mesh2 object
> also allows for smoothly colored triangles, so in that sense there's
> no need to really do it. The big question is really what do you want
> to see and what do get instead?
>
> Cheers,
>
> Tsjerk
>
> On Mon, May 18, 2009 at 4:53 PM, Abhinav Verma <abh...@gm...>
> wrote:
> > Hi Tsjerk,
> >  Thanks a lot for reply.. All I wanted to try was to use povray instead
> of
> > pymol's internal ray tracer. Now if you type "help povray", it will come
> > with a suggestion to use an age old patch and use smooth_color.
> > ----------------------------------------------------
> > PyMOL>help povray
> >
> > DESCRIPTION
> >
> >   PovRay: Persistance of Vision Support Information (EXPERIMENTAL)
> >
> >   The built-in ray-tracer (technically a ray-caster) is as fast or
> >   faster than PovRay for most figures (provided that hash_max is
> >   tuned for your system). However, PovRay blows PyMOL away when it
> >   comes to rendering images without using lots of RAM, and with
> >   PovRay you get the ability use perspective, textures, reflections,
> >   infinite objects, and a superior lighting model.
> >
> >   PovRay does not include interpolated colors within triangles (!!),
> >   so you must patch the source code in order to obtain this basic
> >   functionality required for rendering molecular surfaces. Details
> >   can be found on the DINO website.
> >
> >   " rel="nofollow">http://www.biozentrum.unibas.ch/~xray/dino<http://www.biozentrum.unibas.ch/%7Exray/dino>
> >
> >   To use PovRay, you must be running under Unix and have x-povray in
> >   your path. Unfortunately, the developers of PovRay do not share
> >   PyMOL's open-source philosophy, so you will need to download,
> >   configure, patch (for smooth_color_triangles), and install it
> >   yourself. Despite being free and open-source, PovRay's license
> >   prevents it from being modified or conveniently combined with
> >   PyMOL, and thus it serves as a textbook example for why open-source
> >   licenses should be wholly non-restrictive.
> >
> >   Assuming that PovRay is built and in your path...
> >
> >   ray renderer=1 # will use PovRay instead of the built-in engine
> >
> >   set ray_default_renderer=1 # changes the default renderer to PovRay
> >   ray # will now use PovRay by default
> >
> >   cmd.get_povray() # will give you a tuple of PovRay input strings
> >   # which you can manipulate from Python
> >
> >   set smooth_color_triangles = 1 # is required in order to get decent
> >   surfaces in PovRay. You must patch PovRay first.
> >
> --------------------------------------------------------------------------------------------
> > so I tired that link (the patch was moved since then to another address)
> >
> http://www.mail-archive.com/pym...@li.../msg00868.html
> > but all that is useless since smooth_color_triangle itself doesnt exist.
> I
> > tried to change it to smooth_triangle and still povray didnt do anything.
> So
> > Now I tried your suggestions of manually editing the file and changing
> some
> > settings .. but I am not getting the result yet..
> > I am linking 3 pictures.
> > 1. internal ray tracer (
> >
> http://picasaweb.google.com/lh/photo/c9LUJwzPEYjpVVC0ThkQhQ?feat=directlink
> > )
> > 2. using ray renderer=1 for povray (
> >
> http://picasaweb.google.com/lh/photo/0736f1oK9dRaB8fV7Zmm6g?feat=directlink
> > )
> > 3. applying ur settings (
> >
> http://picasaweb.google.com/lh/photo/udk9a4AzhpdI2RfQvclciw?feat=directlink
> > )
> > Pymol should probably update the "help povray" description so that it
> does
> > not mislead anymore.
> > Thanks !!
> > Abhi
> >
> >
> >
> > On Mon, May 18, 2009 at 11:55 AM, Tsjerk Wassenaar <ts...@gm...>
> > wrote:
> >>
> >> Hi Abhi,
> >>
> >> I had a look and found that POV-Ray does not have a keyword
> >> 'smooth_color_triangle' (anymore), but this should be changed to
> >> 'smooth_triangle'. Also, the mesh2 object Pymol writes already for
> >> ages is far superior to a set of smooth_triangles. This leaves me a
> >> bit puzzled as what it is you mean. Could you link/post an example of
> >> the image as you get now and indicate what you want to have different?
> >> Maybe also try the change in lighting and finish I posted a few days
> >> ago on the list. It may well be that the default POV-Ray settings
> >> pymol uses for light and appearance are causing the problem.
> >>
> >> Cheers,
> >>
> >> Tsjerk
> >>
> >> On Mon, May 11, 2009 at 5:41 PM, Tsjerk Wassenaar <ts...@gm...>
> >> wrote:
> >> > Hi Abhi,
> >> >
> >> > I got and read the e-mail through the list, but would have to test
> >> > with pymol >1.0 before being able to give a sensible reply. As I'm now
> >> > underway that's a bit too much for me :) I'll come back on this one
> >> > later.
> >> > By the way, you only sent this mail this afternoon. Don't expect
> >> > instant replies or assume something didn't come through just because
> >> > you didn't get an answer within a few hours :)
> >> >
> >> > Cheers,
> >> >
> >> > Tsjerk
> >> >
> >> > On Mon, May 11, 2009 at 5:05 PM, Abhinav Verma <abh...@gm...
> >
> >> > wrote:
> >> >> Hi Tsjerk,
> >> >>
> >> >>  I am sending this email personally to you (sorry for that).  I am
> >> >> sorry,
> >> >> but I posted it to pymol mailing list but it seems to have been stuck
> >> >> somewhere.
> >> >>  Any idea would be helpful,
> >> >>
> >> >> thanks,
> >> >> Abhi
> >> >>
> >> >> ---------- Forwarded message ----------
> >> >> From: Abhinav Verma <abh...@gm...>
> >> >> Date: Mon, May 11, 2009 at 3:06 PM
> >> >> Subject: Using povray with pymol
> >> >> To: pymol-users <pym...@li...>
> >> >>
> >> >>
> >> >> I am trying to use povray tracer with pymol. I got povray and
> installed
> >> >> it
> >> >> and tried to follow the instructions for the patch.. The patch seems
> >> >> too old
> >> >> written in 1999 and the current povray code is cpp and not c. so I
> >> >> skipped
> >> >> that part.. and now when I set smooth_color_triangle = 1, I get the
> >> >> following parse error..
> >> >>
> >> >> pigment{color rgb<1.00001,0.0904,0.0000>}}
> >> >> mesh {
> >> >> smooth_color_triangle
> >> >> Parse Error: No triangles in triangle mesh.
> >> >>
> >> >> If I donot swich it on, I get really ugly colored picture from the
> >> >> tmp_povray.pov file generated by pymol.
> >> >> Any Ideas to get  similars colors that comes with pymol inbuild ray
> >> >> tracer
> >> >> and use povray ( I want to use povray as pymol is crashing because of
> >> >> size )
> >> >>
> >> >> Thanks in advance,
> >> >> Abhi
> >> >>
> >> >>
> >> >
> >> >
> >> >
> >> > --
> >> > Tsjerk A. Wassenaar, Ph.D.
> >> > Junior UD (post-doc)
> >> > Biomolecular NMR, Bijvoet Center
> >> > Utrecht University
> >> > Padualaan 8
> >> > 3584 CH Utrecht
> >> > The Netherlands
> >> > P: +31-30-2539931
> >> > F: +31-30-2537623
> >> >
> >>
> >>
> >>
> >> --
> >> Tsjerk A. Wassenaar, Ph.D.
> >> Junior UD (post-doc)
> >> Biomolecular NMR, Bijvoet Center
> >> Utrecht University
> >> Padualaan 8
> >> 3584 CH Utrecht
> >> The Netherlands
> >> P: +31-30-2539931
> >> F: +31-30-2537623
> >
> >
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>

Hi Abhi,

Oooh, that's an oldie alright. I only vaguely recollect that coming in
:) But you need to patch POV-Ray for it... Anyway, the mesh2 object
also allows for smoothly colored triangles, so in that sense there's
no need to really do it. The big question is really what do you want
to see and what do get instead?

Cheers,

Tsjerk

On Mon, May 18, 2009 at 4:53 PM, Abhinav Verma <abh...@gm...> wrote:
> Hi Tsjerk,
>  Thanks a lot for reply.. All I wanted to try was to use povray instead of
> pymol's internal ray tracer. Now if you type "help povray", it will come
> with a suggestion to use an age old patch and use smooth_color.
> ----------------------------------------------------
> PyMOL>help povray
>
> DESCRIPTION
>
>   PovRay: Persistance of Vision Support Information (EXPERIMENTAL)
>
>   The built-in ray-tracer (technically a ray-caster) is as fast or
>   faster than PovRay for most figures (provided that hash_max is
>   tuned for your system). However, PovRay blows PyMOL away when it
>   comes to rendering images without using lots of RAM, and with
>   PovRay you get the ability use perspective, textures, reflections,
>   infinite objects, and a superior lighting model.
>
>   PovRay does not include interpolated colors within triangles (!!),
>   so you must patch the source code in order to obtain this basic
>   functionality required for rendering molecular surfaces. Details
>   can be found on the DINO website.
>
>   http://www.biozentrum.unibas.ch/~xray/dino
>
>   To use PovRay, you must be running under Unix and have x-povray in
>   your path. Unfortunately, the developers of PovRay do not share
>   PyMOL's open-source philosophy, so you will need to download,
>   configure, patch (for smooth_color_triangles), and install it
>   yourself. Despite being free and open-source, PovRay's license
>   prevents it from being modified or conveniently combined with
>   PyMOL, and thus it serves as a textbook example for why open-source
>   licenses should be wholly non-restrictive.
>
>   Assuming that PovRay is built and in your path...
>
>   ray renderer=1 # will use PovRay instead of the built-in engine
>
>   set ray_default_renderer=1 # changes the default renderer to PovRay
>   ray # will now use PovRay by default
>
>   cmd.get_povray() # will give you a tuple of PovRay input strings
>   # which you can manipulate from Python
>
>   set smooth_color_triangles = 1 # is required in order to get decent
>   surfaces in PovRay. You must patch PovRay first.
> --------------------------------------------------------------------------------------------
> so I tired that link (the patch was moved since then to another address)
> http://www.mail-archive.com/pym...@li.../msg00868.html
> but all that is useless since smooth_color_triangle itself doesnt exist. I
> tried to change it to smooth_triangle and still povray didnt do anything. So
> Now I tried your suggestions of manually editing the file and changing some
> settings .. but I am not getting the result yet..
> I am linking 3 pictures.
> 1. internal ray tracer (
> http://picasaweb.google.com/lh/photo/c9LUJwzPEYjpVVC0ThkQhQ?feat=directlink
> )
> 2. using ray renderer=1 for povray (
> http://picasaweb.google.com/lh/photo/0736f1oK9dRaB8fV7Zmm6g?feat=directlink
> )
> 3. applying ur settings (
> http://picasaweb.google.com/lh/photo/udk9a4AzhpdI2RfQvclciw?feat=directlink
> )
> Pymol should probably update the "help povray" description so that it does
> not mislead anymore.
> Thanks !!
> Abhi
>
>
>
> On Mon, May 18, 2009 at 11:55 AM, Tsjerk Wassenaar <ts...@gm...>
> wrote:
>>
>> Hi Abhi,
>>
>> I had a look and found that POV-Ray does not have a keyword
>> 'smooth_color_triangle' (anymore), but this should be changed to
>> 'smooth_triangle'. Also, the mesh2 object Pymol writes already for
>> ages is far superior to a set of smooth_triangles. This leaves me a
>> bit puzzled as what it is you mean. Could you link/post an example of
>> the image as you get now and indicate what you want to have different?
>> Maybe also try the change in lighting and finish I posted a few days
>> ago on the list. It may well be that the default POV-Ray settings
>> pymol uses for light and appearance are causing the problem.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Mon, May 11, 2009 at 5:41 PM, Tsjerk Wassenaar <ts...@gm...>
>> wrote:
>> > Hi Abhi,
>> >
>> > I got and read the e-mail through the list, but would have to test
>> > with pymol >1.0 before being able to give a sensible reply. As I'm now
>> > underway that's a bit too much for me :) I'll come back on this one
>> > later.
>> > By the way, you only sent this mail this afternoon. Don't expect
>> > instant replies or assume something didn't come through just because
>> > you didn't get an answer within a few hours :)
>> >
>> > Cheers,
>> >
>> > Tsjerk
>> >
>> > On Mon, May 11, 2009 at 5:05 PM, Abhinav Verma <abh...@gm...>
>> > wrote:
>> >> Hi Tsjerk,
>> >>
>> >>  I am sending this email personally to you (sorry for that).  I am
>> >> sorry,
>> >> but I posted it to pymol mailing list but it seems to have been stuck
>> >> somewhere.
>> >>  Any idea would be helpful,
>> >>
>> >> thanks,
>> >> Abhi
>> >>
>> >> ---------- Forwarded message ----------
>> >> From: Abhinav Verma <abh...@gm...>
>> >> Date: Mon, May 11, 2009 at 3:06 PM
>> >> Subject: Using povray with pymol
>> >> To: pymol-users <pym...@li...>
>> >>
>> >>
>> >> I am trying to use povray tracer with pymol. I got povray and installed
>> >> it
>> >> and tried to follow the instructions for the patch.. The patch seems
>> >> too old
>> >> written in 1999 and the current povray code is cpp and not c. so I
>> >> skipped
>> >> that part.. and now when I set smooth_color_triangle = 1, I get the
>> >> following parse error..
>> >>
>> >> pigment{color rgb<1.00001,0.0904,0.0000>}}
>> >> mesh {
>> >> smooth_color_triangle
>> >> Parse Error: No triangles in triangle mesh.
>> >>
>> >> If I donot swich it on, I get really ugly colored picture from the
>> >> tmp_povray.pov file generated by pymol.
>> >> Any Ideas to get  similars colors that comes with pymol inbuild ray
>> >> tracer
>> >> and use povray ( I want to use povray as pymol is crashing because of
>> >> size )
>> >>
>> >> Thanks in advance,
>> >> Abhi
>> >>
>> >>
>> >
>> >
>> >
>> > --
>> > Tsjerk A. Wassenaar, Ph.D.
>> > Junior UD (post-doc)
>> > Biomolecular NMR, Bijvoet Center
>> > Utrecht University
>> > Padualaan 8
>> > 3584 CH Utrecht
>> > The Netherlands
>> > P: +31-30-2539931
>> > F: +31-30-2537623
>> >
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>> Junior UD (post-doc)
>> Biomolecular NMR, Bijvoet Center
>> Utrecht University
>> Padualaan 8
>> 3584 CH Utrecht
>> The Netherlands
>> P: +31-30-2539931
>> F: +31-30-2537623
>
>
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Hi Tsjerk,
 Thanks a lot for reply.. All I wanted to try was to use povray instead of
pymol's internal ray tracer. Now if you type "help povray", it will come
with a suggestion to use an age old patch and use smooth_color.
----------------------------------------------------
PyMOL>help povray

DESCRIPTION

  PovRay: Persistance of Vision Support Information (EXPERIMENTAL)

  The built-in ray-tracer (technically a ray-caster) is as fast or
  faster than PovRay for most figures (provided that hash_max is
  tuned for your system). However, PovRay blows PyMOL away when it
  comes to rendering images without using lots of RAM, and with
  PovRay you get the ability use perspective, textures, reflections,
  infinite objects, and a superior lighting model.

  PovRay does not include interpolated colors within triangles (!!),
  so you must patch the source code in order to obtain this basic
  functionality required for rendering molecular surfaces. Details
  can be found on the DINO website.

  http://www.biozentrum.unibas.ch/~xray/dino

  To use PovRay, you must be running under Unix and have x-povray in
  your path. Unfortunately, the developers of PovRay do not share
  PyMOL's open-source philosophy, so you will need to download,
  configure, patch (for smooth_color_triangles), and install it
  yourself. Despite being free and open-source, PovRay's license
  prevents it from being modified or conveniently combined with
  PyMOL, and thus it serves as a textbook example for why open-source
  licenses should be wholly non-restrictive.

  Assuming that PovRay is built and in your path...

  ray renderer=1 # will use PovRay instead of the built-in engine

  set ray_default_renderer=1 # changes the default renderer to PovRay
  ray # will now use PovRay by default

  cmd.get_povray() # will give you a tuple of PovRay input strings
  # which you can manipulate from Python

  set smooth_color_triangles = 1 # is required in order to get decent
  surfaces in PovRay. You must patch PovRay first.
--------------------------------------------------------------------------------------------
so I tired that link (the patch was moved since then to another address)
http://www.mail-archive.com/pym...@li.../msg00868.html
but all that is useless since smooth_color_triangle itself doesnt exist. I
tried to change it to smooth_triangle and still povray didnt do anything. So
Now I tried your suggestions of manually editing the file and changing some
settings .. but I am not getting the result yet..
I am linking 3 pictures.
1. internal ray tracer (
http://picasaweb.google.com/lh/photo/c9LUJwzPEYjpVVC0ThkQhQ?feat=directlink)
2. using ray renderer=1 for povray (
http://picasaweb.google.com/lh/photo/0736f1oK9dRaB8fV7Zmm6g?feat=directlink)
3. applying ur settings (
http://picasaweb.google.com/lh/photo/udk9a4AzhpdI2RfQvclciw?feat=directlink)
Pymol should probably update the "help povray" description so that it does
not mislead anymore.
Thanks !!
Abhi




On Mon, May 18, 2009 at 11:55 AM, Tsjerk Wassenaar <ts...@gm...>wrote:

> Hi Abhi,
>
> I had a look and found that POV-Ray does not have a keyword
> 'smooth_color_triangle' (anymore), but this should be changed to
> 'smooth_triangle'. Also, the mesh2 object Pymol writes already for
> ages is far superior to a set of smooth_triangles. This leaves me a
> bit puzzled as what it is you mean. Could you link/post an example of
> the image as you get now and indicate what you want to have different?
> Maybe also try the change in lighting and finish I posted a few days
> ago on the list. It may well be that the default POV-Ray settings
> pymol uses for light and appearance are causing the problem.
>
> Cheers,
>
> Tsjerk
>
> On Mon, May 11, 2009 at 5:41 PM, Tsjerk Wassenaar <ts...@gm...>
> wrote:
> > Hi Abhi,
> >
> > I got and read the e-mail through the list, but would have to test
> > with pymol >1.0 before being able to give a sensible reply. As I'm now
> > underway that's a bit too much for me :) I'll come back on this one
> > later.
> > By the way, you only sent this mail this afternoon. Don't expect
> > instant replies or assume something didn't come through just because
> > you didn't get an answer within a few hours :)
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On Mon, May 11, 2009 at 5:05 PM, Abhinav Verma <abh...@gm...>
> wrote:
> >> Hi Tsjerk,
> >>
> >>  I am sending this email personally to you (sorry for that).  I am
> sorry,
> >> but I posted it to pymol mailing list but it seems to have been stuck
> >> somewhere.
> >>  Any idea would be helpful,
> >>
> >> thanks,
> >> Abhi
> >>
> >> ---------- Forwarded message ----------
> >> From: Abhinav Verma <abh...@gm...>
> >> Date: Mon, May 11, 2009 at 3:06 PM
> >> Subject: Using povray with pymol
> >> To: pymol-users <pym...@li...>
> >>
> >>
> >> I am trying to use povray tracer with pymol. I got povray and installed
> it
> >> and tried to follow the instructions for the patch.. The patch seems too
> old
> >> written in 1999 and the current povray code is cpp and not c. so I
> skipped
> >> that part.. and now when I set smooth_color_triangle = 1, I get the
> >> following parse error..
> >>
> >> pigment{color rgb<1.00001,0.0904,0.0000>}}
> >> mesh {
> >> smooth_color_triangle
> >> Parse Error: No triangles in triangle mesh.
> >>
> >> If I donot swich it on, I get really ugly colored picture from the
> >> tmp_povray.pov file generated by pymol.
> >> Any Ideas to get  similars colors that comes with pymol inbuild ray
> tracer
> >> and use povray ( I want to use povray as pymol is crashing because of
> size )
> >>
> >> Thanks in advance,
> >> Abhi
> >>
> >>
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > Junior UD (post-doc)
> > Biomolecular NMR, Bijvoet Center
> > Utrecht University
> > Padualaan 8
> > 3584 CH Utrecht
> > The Netherlands
> > P: +31-30-2539931
> > F: +31-30-2537623
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>

Hi Abhi,

I had a look and found that POV-Ray does not have a keyword
'smooth_color_triangle' (anymore), but this should be changed to
'smooth_triangle'. Also, the mesh2 object Pymol writes already for
ages is far superior to a set of smooth_triangles. This leaves me a
bit puzzled as what it is you mean. Could you link/post an example of
the image as you get now and indicate what you want to have different?
Maybe also try the change in lighting and finish I posted a few days
ago on the list. It may well be that the default POV-Ray settings
pymol uses for light and appearance are causing the problem.

Cheers,

Tsjerk

On Mon, May 11, 2009 at 5:41 PM, Tsjerk Wassenaar <ts...@gm...> wrote:
> Hi Abhi,
>
> I got and read the e-mail through the list, but would have to test
> with pymol >1.0 before being able to give a sensible reply. As I'm now
> underway that's a bit too much for me :) I'll come back on this one
> later.
> By the way, you only sent this mail this afternoon. Don't expect
> instant replies or assume something didn't come through just because
> you didn't get an answer within a few hours :)
>
> Cheers,
>
> Tsjerk
>
> On Mon, May 11, 2009 at 5:05 PM, Abhinav Verma <abh...@gm...> wrote:
>> Hi Tsjerk,
>>
>>  I am sending this email personally to you (sorry for that).  I am sorry,
>> but I posted it to pymol mailing list but it seems to have been stuck
>> somewhere.
>>  Any idea would be helpful,
>>
>> thanks,
>> Abhi
>>
>> ---------- Forwarded message ----------
>> From: Abhinav Verma <abh...@gm...>
>> Date: Mon, May 11, 2009 at 3:06 PM
>> Subject: Using povray with pymol
>> To: pymol-users <pym...@li...>
>>
>>
>> I am trying to use povray tracer with pymol. I got povray and installed it
>> and tried to follow the instructions for the patch.. The patch seems too old
>> written in 1999 and the current povray code is cpp and not c. so I skipped
>> that part.. and now when I set smooth_color_triangle = 1, I get the
>> following parse error..
>>
>> pigment{color rgb<1.00001,0.0904,0.0000>}}
>> mesh {
>> smooth_color_triangle
>> Parse Error: No triangles in triangle mesh.
>>
>> If I donot swich it on, I get really ugly colored picture from the
>> tmp_povray.pov file generated by pymol.
>> Any Ideas to get  similars colors that comes with pymol inbuild ray tracer
>> and use povray ( I want to use povray as pymol is crashing because of size )
>>
>> Thanks in advance,
>> Abhi
>>
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Hi Hirdesh,

You don't say what you have, what you want to show and what you tried
to show it. So we can't help you. I would also politely like you to
consider that perhaps we might not be very apt to do your work for
you. We're willing to help though, when you run into problems doing
your own work or when you can't find a solution to your problems in
the user list archives or on the wiki.

Cheers,

Tsjerk

On Sun, May 17, 2009 at 8:40 AM, hirdesh kumar <hir...@gm...> wrote:
> Hi All,
> I want to prepare movie for my presentation representing various properties
> of protein and bound ligand.  Can anyone help me for the same
>
> --
> Hirdesh Kumar Sharma
> M.S. (Pharm) Final Semester
> Centre for Pharmacoinformatics
> A-212; Research Block A
> NIPER,
> Sector 67, S.A.S. Nagar, Mohali
> Punjab-160062, INDIA
>
> ------------------------------------------------------------------------------
> Crystal Reports - New Free Runtime and 30 Day Trial
> Check out the new simplified licensing option that enables
> unlimited royalty-free distribution of the report engine
> for externally facing server and web deployment.
> http://p.sf.net/sfu/businessobjects
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Hi All,
I want to prepare movie for my presentation representing various properties
of protein and bound ligand.  Can anyone help me for the same

-- 
Hirdesh Kumar Sharma
M.S. (Pharm) Final Semester
Centre for Pharmacoinformatics
A-212; Research Block A
NIPER,
Sector 67, S.A.S. Nagar, Mohali
Punjab-160062, INDIA

Hi Tom,

Just as Robert says, the quote should be dropped. Maybe you should've
had just one coffee more, but I should also have been more careful
typing. Apparently I usually automatically start of with typing
strings after .write( ;)

Sorry about that.

Tsjerk

On Fri, May 15, 2009 at 11:57 PM, Thomas Stout <ts...@ex...> wrote:
>
>
> Hi Tsjerk --
>
> What version of PyMOL does this work with?  I've been trying your commands
> with versions 1.1 and 1.2b and while PyMOL reports that the primitives have
> been processed, nothing is written to the file "protein.pov" other than the
> header info:
>
>      camera {orthographic location <0.0 , 0.0 , 134.1048736572>
>      look_at  <0.0 , 0.0 , -1.0> right -74.9812240601*x up 59.9849815369*y}
>      #default { finish{phong   -1.000 ambient    0.500 diffuse    0.450
> phong_size 13
>      .750000}}
>      light_source{<4000.0001,4000.0001,9865.8951>  rgb<1.0,1.0,1.0>}
>      plane{z , -206.0869
>       pigment{color rgb<1.0000,1.0000,1.0000>}
>       finish{phong 0 specular 0 diffuse 0 ambient 1.0}}
>      #include "povray.inc"
>
> and povray.inc contains:
>      cmd.get_povray()[1]
>
> If I save a povray file with the GUI menu selection: File> Save Image As>
> POV-Ray
> then I get everything written to disk.  This occurs on both linux and
> Windows.
>
> Am I missing something that would be more obvious if I had had more coffee
> today?
>
> Thanks!
> -Tom
>
> PS - There was a missing quotation mark:
> open("povray.inc","w").write("cmd.get_povray()[1]) -->
> open("povray.inc","w").write("cmd.get_povray()[1]")
>
>
>
> -----Original Message-----
> From: Tsjerk Wassenaar [mailto:ts...@gm...]
> Sent: Thu 5/14/2009 1:47 PM
> To: Sean Law
> Cc: pymol-users
> Subject: Re: [PyMOL] POVRAY Usage
>
> Hi Sean,
>
> Unfortunately, getting a good image through POV-Ray requires editing
> the POV-Ray file. You can write the scene to disk with the following
> commands
>
> pov=open("protein.pov","w")
> pov.write(cmd.get_povray()[0])
> pov.write("#include \"povray.inc\"")
> pov.close()
>
> open("povray.inc","w").write("cmd.get_povray()[1])
>
> Then, take your favorite editor (under windows, you can use the
> POV-Ray editor) and make some changes:
>
> 1. There's a line starting with #defaults. Remove that and replace it with:
>
> #default {
>     finish {
>         ambient .15
>         diffuse .5
>         specular 1
>         roughness .001
>         reflection { .5 metallic } // Remove this line for less
> glossyness and faster tracing
>     }
> }
>
> 2. There's a light statement, which says:
> light_source{<4000.0001,4000.0001,9960.0000>  rgb<1.0,1.0,1.0>}.
> Replace it with:
>
> light_source
> {
>    <20,10,0>
>    rgb 2
>    area_light <5,5,0>,5,5
>    adaptive 1
>    jitter
> }
>
> This usually works for me :)
>
> Note that the trace may now take some time. Remove the metallic
> reflection for faster tracing.
>
> I hope it helps. POV-Ray is cool, but rather complicated.
>
> Cheers,
>
> Tsjerk
>
> On Thu, May 14, 2009 at 10:21 PM, Sean Law <mag...@ho...> wrote:
>>
>> Hi All,
>>
>> While ray tracing a scene with 10 x-large proteins in grid mode at 3600,
>> 3600 (width, height) I ran out of RAM (2 GB).  I tried it again by writing
>> everything into a script and using pymol -qc which still ran out of memory.
>> I read somewhere that POVRAY is less of a memory hog so I installed the
>> latest version and simply modified my script to "ray 3600, 3600, renderer=1"
>> to use POVRAY.  Everything went smoothly but I noticed that the image
>> generated from POVRAY looked different than the native ray traced structure
>> using PyMOL's ray tracer (simply invoking "ray" without dimensions in
>> PyMOL).  Specifically, the light reflections appeared to be dulled in POVRAY
>> and spheres that were further away from the camera view are not
>> distinguishable.  I've posted a comparison on the PyMOLWiki:
>>
>> http://www.pymolwiki.org/index.php/Povray_vs._pymol
>>
>> Firstly, I apologize as I am completely new to the world of POVRAY and I
>> just assumed that the image produced from either method would give
>> identical/close results but I much prefer the look of the PyMOL ray-tracer.
>> Is there an easy way to set everything up the same way as the PyMOL
>> ray-tracer but for POVRAY?  Thank you for your time.
>>
>> Sean
>>
>> ________________________________
>> Help keep personal info safe. Get Internet Explorer 8 today!
>>
>> ------------------------------------------------------------------------------
>> The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
>> production scanning environment may not be a perfect world - but thanks to
>> Kodak, there's a perfect scanner to get the job done! With the NEW KODAK
>> i700
>> Series Scanner you'll get full speed at 300 dpi even with all image
>> processing features enabled. http://p.sf.net/sfu/kodak-com
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>
> ------------------------------------------------------------------------------
> The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
> production scanning environment may not be a perfect world - but thanks to
> Kodak, there's a perfect scanner to get the job done! With the NEW KODAK
> i700
> Series Scanner you'll get full speed at 300 dpi even with all image
> processing features enabled. http://p.sf.net/sfu/kodak-com
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
> This email (including any attachments) may contain material
> that is confidential and privileged and is for the sole use of
> the intended recipient. Any review, reliance or distribution by
> others or forwarding without express permission is strictly
> prohibited. If you are not the intended recipient, please
> contact the sender and delete all copies.
> Exelixis, Inc. reserves the right, to the extent and under
> circumstances permitted by applicable law, to retain, monitor
> and intercept e-mail messages to and from its systems.
>
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623