pymol-users

[PyMOL] Movie making questions

[Yuri <yur...@uf...>]

Dear Users,
I was putting together some movies using pymol and I have some 
questions.
First, how can I gradually make a surface go from solid to transparent? 
Currently what I see is, in scene 1 I have it solid (0% transp.) 
surface. Then after I show some ligands and aa side chains in scene 2, I 
try to get the surface to look transparent (60%) in scene 3.
However when I reinterpolate and play the movie every surface will be 
60%, the last setting I entered.
Second, how can I make an object (ligand shown as stciks) rotate or 
flip? I can make it move using "translate" but this happens in a linear 
fashion.
Lastly, I like to save movies as pngs and later create the movie. How 
can I change the output frame size, e.g. 1024x1024?

Thank you so much for your time,

-- 
Yuri Pompeu

Re: [PyMOL] Movie making questions

[Thomas H. <sp...@us...>]

Hi Yuri,

> I was putting together some movies using pymol and I have some 
> questions.
> First, how can I gradually make a surface go from solid to transparent? 
> Currently what I see is, in scene 1 I have it solid (0% transp.) 
> surface. Then after I show some ligands and aa side chains in scene 2, I 
> try to get the surface to look transparent (60%) in scene 3.
> However when I reinterpolate and play the movie every surface will be 
> 60%, the last setting I entered.

looks like scenes do not save settings. What you need is the "mdo" 
command to register the transparency with a particular movie frame.

http://pymolwiki.org/index.php/Mdo

Example:
mdo 1: set transparency, 0.0
mdo 100: set transparency, 0.6

This might also be interesting for you:
http://pymolwiki.org/index.php/Movie_fade

> Second, how can I make an object (ligand shown as stciks) rotate or 
> flip? I can make it move using "translate" but this happens in a linear 
> fashion.

not sure about this right now, but does "matrix_mode" make a difference?

set matrix_mode, 1

See:
http://www.pymolwiki.org/index.php/MovieSchool_5#Object_Motions

> Lastly, I like to save movies as pngs and later create the movie. How 
> can I change the output frame size, e.g. 1024x1024?

viewport 1024, 1024

http://www.pymolwiki.org/index.php/Viewport

Hope that helps.

Cheers,
   Thomas

--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen