Re: [PyMOL] Smooth fading of surface in movie?

[Dirk K. <kos...@ge...>]

Dear PyMOLers,

thanks a lot to all of you for your helpful suggestions! I will try  
Tsjerk's way that probably keeps me from writing an external Fortran  
program for generating pymol commands ;-)

Best regards,

Dirk.

Am 01.09.2009 um 20:42 schrieb Tsjerk Wassenaar:

> Hi :)
>
> Some people are just not lazy enough ;) Lazy people like me spend a
> good deal of effort thinking about how to avoid efforts like writing
> repetitive lines :p And then you could come up with:
>
> from math import sin,pi
> mset 1 x300
> for i in range(200,301): cmd.mdo( i, "set transparency,selection,%f" %
> ( math.sin( math.pi*(i-200)/(2*100) ) ) )
>
> The fuzz with the sine is of course to have a smoother fade. One could
> also take the simpler linear fade, but mind that the either numerator
> or divisor (or both) have to be float in order to end up with a float:
>
> for i in range(200,301): cmd.mdo( i, "set transparency,selection,%f" %
> ( (i-200)/100.0 ) )
>
> With a bit more scripting, you can easily use this to define functions
> for fading properties from one value to another over a given range of
> frames.
>
> As a side note, if the fade is part of a more complex movie, hide the
> surface one frame after the fade has completed. Possibly it's also
> best to explicitly show it again in the first frame, in case you have
> Pymol cycle through the movie. In case the purpose is fading in the
> surface, start with surface view hidden and turn on the surface the
> frame before you start the fade. This way you avoid Pymol calculating
> its way through a null surface, possibly even coming up with some
> artefacts...
>
> Hope it helps,
>
> Tsjerk
>
>
> On Tue, Sep 1, 2009 at 5:01 PM, Matthew D. Hogg<mh...@uv...> wrote:
>> I use a clunky set of mdo commands to do this.
>>
>> mdo 266: set transparency, .1, (palm+linker+Nterm)
>> mdo 267: set transparency, .2, (palm+linker+Nterm)
>> mdo 268: set transparency, .3, (palm+linker+Nterm)
>> mdo 269: set transparency, .4, (palm+linker+Nterm)
>> mdo 270: set transparency, .5, (palm+linker+Nterm)
>> mdo 271: set transparency, .6, (palm+linker+Nterm)
>> mdo 272: set transparency, .7, (palm+linker+Nterm)
>> mdo 273: set transparency, .8, (palm+linker+Nterm)
>> mdo 274: set transparency, .9, (palm+linker+Nterm)
>> mdo 275: set transparency, 1, (palm+linker+Nterm)
>>
>> If the surfaces are turned on for objects palm, linker and Nterm,  
>> then
>> this will fade out the surface over frames 266 to 275. Setting the
>> transparency to 1 and then reversing the order of the values will  
>> make
>> the surface fade in.
>>
>> HTH
>>
>> Matthew Hogg
>> University of Vermont
>> Burlington, VT 05405
>>
>>
>> Quoting Dirk Kostrewa <kos...@ge...>:
>>
>>> 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:       kos...@ge...
>>> WWW:  www.genzentrum.lmu.de
>>> *******************************************************
>>
>>
>>
>>
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>
>
>
> -- 
> 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
>
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*******************************************************
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:	kos...@ge...
WWW:	www.genzentrum.lmu.de
*******************************************************