A silly but working solution is to embed the pymol script in a csh script which changes the value for the transparency in small steps.

Not ellegant but if you know csh/sh/bash it's easy. 

A. 

Sent from my iPhone

On 1 Sep 2009, at 16:23, "Schubert, Carsten [PRDUS]" <CSCHUBER@its.jnj.com> wrote:

That would require execution of a python program within a specific scene, which is not supported as far as I know. Scenes are intended to be static representations of display states, for lack of a better word. You would need to manually run the fade script before transitioning the scene. Not sure if this is what you want. Looks as if you may be better off plunging into movies if you really need the effect.

 

Mark Lutz, David Asher , Learning Python, o’Reilly .... Great book if you want to dive into python.

 

Cheers,

 

                Carsten

 

From: Dirk Kostrewa [mailto:kostrewa@genzentrum.lmu.de]
Sent: Tuesday, September 01, 2009 9:56 AM
To: PyMOLBB
Subject: Re: [PyMOL] Smooth fading of surface in movie?

 

Dear Carsten,

 

yes, thanks. However, for a smooth fading, that would require a lot of scenes. Is there a simple python loop, that would create scenes with smooth transparency fading-in from 0 to 1 and that I could use in my pymol-scripts? Unfortunately, I'm not familiar with python, yet ...

 

Best regards,

 

Dirk.

 

Am 01.09.2009 um 15:39 schrieb Schubert, Carsten [PRDUS]:



Dirk,

 

you could try playing around with different transparency settings in subsequent scenes to emulate the effect.

 

HTH

 

Carsten

 

From: Dirk Kostrewa [mailto:kostrewa@genzentrum.lmu.de] 
Sent: Tuesday, September 01, 2009 8:57 AM
To: PyMOLBB
Subject: [PyMOL] Smooth fading of surface in movie?

 

Dear Warren,

 

using PyMOL without any additional "plug-ins", like slerpy or eMovie, is it possible to fade in or out a surface of, say, a ligand, between scenes?

 

Best regards,

 

Dirk.


*******************************************************
Dirk Kostrewa
Gene Center, A 5.07
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone:           +49-89-2180-76845
Fax:    +49-89-2180-76999
E-mail:            kostrewa@genzentrum.lmu.de
WWW:            www.genzentrum.lmu.de
*******************************************************


 

 


*******************************************************
Dirk Kostrewa
Gene Center, A 5.07
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone:           +49-89-2180-76845
Fax:    +49-89-2180-76999
E-mail:            kostrewa@genzentrum.lmu.de
WWW:            www.genzentrum.lmu.de
*******************************************************

 

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