Re: [PyMOL] Making transparent boxes with colored surfaces?

[Dean W. <wa...@ch...>]

Hi Tsjerk,

It works Great!  Thanks so much. I'll have to study your code to see  
where I was going wrong.

Dean

On Apr 23, 2008, at 10:39 AM, Tsjerk Wassenaar wrote:

> Hi Dean,
>
> Funny, really. Last week I was just playing around a bit with creating
> boxes in pymol, e.g. to create a bounding box, and I wanted to have it
> transparent. So here's a script, giving you a function 'rect', which
> takes two tuples, specifying the far edges of the box:
>
> rect( [x0,y0,z0], [x1,y1,z1],name="box",rgbt=[1,1,0,0.5])
>
> The rgbt argument specifies the color and transparency. Feel free to
> go through the code to see how things are done (although you won't
> hear me say it's perfect). In case you have any suggestions, also feel
> free to contact me, either on or off list.
>
> I hope it helps. Cheers,
>
> Tsjerk
>
> On Wed, Apr 23, 2008 at 5:22 PM, Dean Waldow <wa...@ch...>  
> wrote:
>>  Hi Folks,
>>
>> I am very new to pymol and have been learning a lot about using  
>> (mac)pymol.
>> However, I seem to be unable to make a box which is transparent  
>> and has
>> color. I have been able to make a box with the *.py script below  
>> but when I
>> do the ray tracing to get a nice image the box turns to grey /  
>> black. I have
>> also been able to to make prolate and oblate spheriods using ideas  
>> from the
>> pymol wiki.
>>
>> My eventual goal is to have about three slabs or boxes with  
>> spheroids at the
>> interface of these slabs and my pdb results from a monte carlo  
>> simulation
>> where the spheriods highlight the changes in shape of my  
>> copolymers at the
>> interface.
>>
>> Has anyone succeeded in making colored transparent boxes? Or might  
>> there be
>> another strategy?
>>
>> Thanks,
>>
>> Dean Waldow
>>
>> Here is the script (modified from one that makes a bounding box I  
>> believe)
>> that makes my current solid box which turns grey with I issue the ray
>> command:
>>
>>
>> from pymol.cgo import *
>> from pymol import cmd
>> #
>> # SEGMENT     1
>> box = [
>>    LINEWIDTH, 1.0,
>>    BEGIN, VERTEX,
>>    COLOR, 0.0, 0.0, 0.0,
>>
>> # Face 1
>>    VERTEX,   55.000,   55.000,   55.000,
>>    VERTEX,   55.000,    5.000,   55.000,
>>    VERTEX,   55.000,    5.000,    5.000,
>>
>>    VERTEX,   55.000,    5.000,    5.000,
>>    VERTEX,   55.000,   55.000,    5.000,
>>    VERTEX,   55.000,   55.000,   55.000,
>>
>> # Face 2
>>    VERTEX,    5.000,   55.000,   55.000,
>>    VERTEX,    5.000,    5.000,   55.000,
>>    VERTEX,    5.000,    5.000,    5.000,
>>
>>    VERTEX,    5.000,    5.000,    5.000,
>>    VERTEX,    5.000,   55.000,    5.000,
>>    VERTEX,    5.000,   55.000,   55.000,
>>
>> # Face 3
>>    VERTEX,   55.000,   55.000,   55.000,
>>    VERTEX,    5.000,   55.000,   55.000,
>>    VERTEX,    5.000,   55.000,    5.000,
>>
>>    VERTEX,    5.000,   55.000,    5.000,
>>    VERTEX,   55.000,   55.000,    5.000,
>>    VERTEX,   55.000,   55.000,   55.000,
>>
>> # Face 4
>>    VERTEX,   55.000,    5.000,   55.000,
>>    VERTEX,    5.000,    5.000,   55.000,
>>    VERTEX,    5.000,    5.000,    5.000,
>>
>>    VERTEX,    5.000,    5.000,    5.000,
>>    VERTEX,   55.000,    5.000,    5.000,
>>    VERTEX,   55.000,    5.000,   55.000,
>>
>> # Face 5
>>    VERTEX,   55.000,   55.000,   55.000,
>>    VERTEX,    5.000,   55.000,   55.000,
>>    VERTEX,    5.000,    5.000,   55.000,
>>
>>    VERTEX,    5.000,    5.000,   55.000,
>>    VERTEX,   55.000,    5.000,   55.000,
>>    VERTEX,   55.000,   55.000,   55.000,
>>
>> # Face 6
>>    VERTEX,   55.000,   55.000,    5.000,
>>    VERTEX,    5.000,   55.000,    5.000,
>>    VERTEX,    5.000,    5.000,    5.000,
>>
>>    VERTEX,    5.000,    5.000,    5.000,
>>    VERTEX,   55.000,    5.000,    5.000,
>>    VERTEX,   55.000,   55.000,    5.000,
>>
>>    END
>>    ]
>>
>> obj = box
>>
>> cmd.load_cgo(obj,'segment',   1)
>>
>>
>>
>> --
>>
>> --------------------------------------------------------------------- 
>> ---
>>
>> Dean Waldow, Professor               (253) 535-7533
>>
>> Department of Chemistry              (253) 536-5055 (FAX)
>>
>> Pacific Lutheran University          wa...@ch...
>>
>> Tacoma, WA  98447   USA              http://www.chem.plu.edu/waldow/
>>
>> --------------------------------------------------------------------- 
>> ---
>>
>> ---> CIRRUS and the Chemistry homepage: <http://www.chem.plu.edu/>  
>> <----
>>
>> --------------------------------------------------------------------- 
>> ---
>>
>>
>>
>>
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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<rect.py>

-- 
------------------------------------------------------------------------
Dean Waldow, Professor               (253) 535-7533
Department of Chemistry              (253) 536-5055 (FAX)
Pacific Lutheran University          wa...@ch...
Tacoma, WA  98447   USA              http://www.chem.plu.edu/waldow/
------------------------------------------------------------------------
---> CIRRUS and the Chemistry homepage: <http://www.chem.plu.edu/> <----
------------------------------------------------------------------------