RE: [PyMOL] Coloring surfaces by distance

[Warren DeLano]

Peter,

Assuming you have an existing selection

   load my_prot.pdb
   select my_sel, resi 100

You can use the within/of operation...

   color cyan, my_prot within 15 of my_sel
   color red, my_prot within 10 of my_sel

If you needed to exclude the region immediately around the selection, you
could do so with

   color green, (my_prot within 7 of my_sel) and not (my_sel expand 4)

By residue is also an option for coloring complete residues.

   color yellow, byres (my_prot within 7 of my_sel) 

Cheers,
Warren

--
mailto:war...@delsci.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020
  

> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net 
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
> Peter Teriete
> Sent: Tuesday, June 22, 2004 8:33 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Coloring surfaces by distance
> 
> Hi All,
>  
> I know there was a question regarding this some time ago, but 
> didn't see any reply saying how to do it or a suggesting a 
> possible workaround.
>  
> I have a surface coloured by the underlying residues and am 
> wondering if it is possible to colour an additional part of 
> the surface if it's within a certain distance of the selected 
> residues. 
>  
> Thanks,
>  
> Peter
>  
>  
> Dr Peter Teriete
> Laboratory of Molecular Biophysics
> Department of Biochemistry
> University of Oxford
> South Parks Rd.
> Oxford
> OX1 3QU
>  
> Tel: +44 1865 275742
> Fax: +44 1865 275182
>  
> 

[PyMOL] Coloring surfaces by distance

[Peter Teriete]

Hi All,
 
I know there was a question regarding this some time ago, but didn't see
any reply
saying how to do it or a suggesting a possible workaround.
 
I have a surface coloured by the underlying residues and am wondering if
it is possible
to colour an additional part of the surface if it's within a certain
distance of the selected
residues. 
 
Thanks,
 
Peter
 
 
Dr Peter Teriete
Laboratory of Molecular Biophysics
Department of Biochemistry
University of Oxford
South Parks Rd.
Oxford
OX1 3QU
 
Tel: +44 1865 275742
Fax: +44 1865 275182
 

Re: [PyMOL] coloring surfaces

[Robert Campbell]

Rajarshi and Gareth,

* Gareth Stockwell  [2003-04-02 08:40] wrote:
> Rajarshi,
> 
> With a bit of work you could add such a feature to the script, by using
> compiled graphics objects (CGOs).  The PyMOL documentation explains how
> to use them.
> 
> Gareth
> 
> On Tue, 2003-04-01 at 21:42, Rajarshi Guha wrote:
> > Hi,
> >   using the color_b.py script its possible to color the surface of a 
> > molecule. 
> > Is there anyway that an indicator of the spectrum (such as a colored 
> > vertical 
> > bar showing the colors corresponding for the smallest B value to the 
> > highest 
> > B value)
> > 
> > Rajarshi Guha   

As author of the color_b.py script I'll look in to trying to do this.
The problem with CGO objects, as I understand them, is that they are
meant to move with the scene -- one of the real limitations of CGO
labels. I don't think it is possible keep the colour bar in a fixed
orientation, so one would have to reposition it perpendicular to the
direction of view after the fact for making an image.  

If anyone has an alternate method, I'd be happy to hear it.

Cheers,
Robert
-- 
Robert L. Campbell, Ph.D. 
Senior Research Associatephone: 613-533-6821
Dept. of Biochemistry, Queen's University, fax: 613-633-2497
Kingston, ON K7L 3N6  Canada   http://adelie.biochem.queensu.ca/~rlc
PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

Re: [PyMOL] coloring surfaces

[Gareth Stockwell]

Rajarshi,

With a bit of work you could add such a feature to the script, by using
compiled graphics objects (CGOs).  The PyMOL documentation explains how
to use them.

Gareth


On Tue, 2003-04-01 at 21:42, Rajarshi Guha wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
> 
> Hi,
>   using the color_b.py script its possible to color the surface of a 
> molecule. 
> Is there anyway that an indicator of the spectrum (such as a colored vertical 
> bar showing the colors corresponding for the smallest B value to the highest 
> B value)
> 
> Thanks,
> 
> - -- 
> - ---
> Rajarshi Guha   
> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04  06F7 1BB9 E634 9B87 56EE
> - ---
> A man is known by the company he organizes.
>   -- Ambrose Bierce
> 
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.0.7 (GNU/Linux)
> 
> iD8DBQE+ifm6G7nmNJuHVu4RAitoAJ0W/z0veZH1kFaqT4bHjUmeXZVgjgCfW/a9
> 89MzVJBPsepucUIgSSJdlXg=
> =/zYa
> -END PGP SIGNATURE-
> 
> 
> 
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-- 
-
 Gareth Stockwell
 EMBL - European Bioinformatics Institute
 Wellcome Trust Genome Campus
 Hinxton
 Cambridge CB10 1SD  
gar...@ebi.ac.uk
 Tel (+44) 01223 492548  
http://www.ebi.ac.uk/~gareth

[PyMOL] coloring surfaces

[Rajarshi Guha]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi,
  using the color_b.py script its possible to color the surface of a molecule. 
Is there anyway that an indicator of the spectrum (such as a colored vertical 
bar showing the colors corresponding for the smallest B value to the highest 
B value)

Thanks,

- -- 
- ---
Rajarshi Guha   
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04  06F7 1BB9 E634 9B87 56EE
- ---
A man is known by the company he organizes.
-- Ambrose Bierce

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89MzVJBPsepucUIgSSJdlXg=
=/zYa
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