Re: [PyMOL] Draw a colored sphere from cartesian coordinates

[Tsjerk W. <ts...@gm...>]

Hi Horacio, Jason,

I'd definitely go for the pseudoatom way, particularly because
(pseudo)atoms are much more flexible than CGO. I also assume that you
have lots of those lines. Now if you have that in a file xyze.dat,
then you can "simply" (cut 'n paste ;)) do:

for i in open('xyze.dat'): (lambda x:
cmd.pseudoatom(pos=x[0:3],b=x[3]))([float(j) for j in i.split()])

In a script you can better write it out, to make more clear what happens:

for i in open('xyze.dat'):
    x = [float(j) for j in i.split()]
    cmd.pseudoatom(pos=x[0:3],b=x[3])

Then you can color the stuff with spectrum.

Hope it helps.

Cheers,

Tsjerk

2010/1/14 Jason Vertrees <jas...@sc...>:
> Horacio,
>
> If you're asking how to create spheres positioned at some specific
> coordinate, and colored according to some energy, you have two ways to
> accomplish this.
>
> (1) You can take advantage of the pseudoatom command.  In PyMOL type,
> "help pseudoatom" and also read the PyMOL wiki webpage on the
> pseudoatom command (http://pymolwiki.org/index.php/Pseudoatom).
>
>  # simple pseudoatom from your two data lines:
>  pseudoatom aa, pos=[23.4, 54.6, 12.3], b=-123.5
>  pseudoatom bb, pos=[54.5, 23.1, 9.45], b=-56.7
>  zoom *, 10
>  spectrum b
>
> (2) You can create CGO (compiled graphics objects), low-level graphics
> objects.  See the documentation or the PyMOLWiki -- search for "CGO"
> or "compiled graphics objects".  This will be more difficult as you
> will have to turn the energies into colors by hand.
>
> Hope this helps,
>
> -- Jason
>
>
> 2010/1/13 Horacio Pérez-Sánchez <hor...@ki...>:
>> Hi,
>>
>> I was looking in the wiki how to convert the following information about
>> beads, cartesian coordinates + energy :
>>
>> 23.4 54.6 12.3 -123.5
>> 54.5 23.1 9.45 -56.7
>> .......
>>
>> to a draw in pymol that contains for each atom a sphere of radius R,
>> centered on its coordinates, and with color, in a rainbow gradient.
>>
>> Thanks
>>
>> Horacio
>>
>>
>>
>>
>>
>>
>>
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>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>
> ------------------------------------------------------------------------------
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> world's best and brightest in the field, creating opportunities for Conference
> attendees to learn about information security's most important issues through
> interactions with peers, luminaries and emerging and established companies.
> http://p.sf.net/sfu/rsaconf-dev2dev
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist