Re: [PyMOL] Help for surface coloring

I have a slightly different answer using (almost:) only PyMOL commands:

# take 1acb as example
fetch 1acb, async=0
import numpy
# center is [x0,y0,z0]
x0,y0,z0=[1,2,3]
alldist = []
iterate_state 1,  1acb, 
alldist.append(numpy.sqrt(numpy.sum([(x-x0)**2,(y-y0)**2,(z-z0)**2])))
# assign dist to b-factors!
di = iter(alldist)
alter 1acb, b=di.next()
spectrum b, rainbow, 1acb

The distance computation line is awkward. I thought of using distance() 
command to replace it. It is also much faster to use distance(). But I 
failed to dig distance values out of the object generated by distance(). 
Anybody knows how to do that?

cheers,hongbo

On 28.07.2011 5:06, Thomas Holder wrote:
> Hi Robert,
>
> you can set the distance between each atom and the center as b-factor, 
> and then use spectrum (or spectrumany [1]) for coloring.
>
> I wrote a small python script that will do that, see attachment.
>
> Example (in PyMOL command line):
>
> run distancecoloring.py
> centerdistance2b (all)
> spectrum b, blue_white_red, (all)
>
> Cheers,
>   Thomas
>
> [1] http://pymolwiki.org/index.php/Spectrumany
>
> On 07/28/2011 04:29 PM, Muench, Robert wrote:
>> Dear community,
>>
>> I was searching the internet for several days now to find out how to
>> perform a distance dependent coloring in pymol.
>>
>> The idea is to color the surface of a viral (spherical) structure. I
>> would like to define the xyz-coordinates of the center of the viral
>> structure an color all residues with a gradient depending on the
>> distance from these xyz coordinates.
>>
>> Can anyone please help me out?
>>
>> All the best
>>
>> Robert
>>
>> *Robert Münch***
>>
>> ---------------------------------------------------------
>>
>> Dipl. Biologist / PhD-Student
>>
>> *Paul-Ehrlich-Institut*
>>
>> Federal Institute for Vaccines and Biomedicines
>>
>> Division of Medical Biotechnology
>>
>> Section 6/5 - Viral Gene Transfer Medicinal Products
>>
>> 63225 Langen, Germany
>>
>> Phone: +49-6103-77-4222
>>
>> Fax: +49-6103-77-1255
>
>
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