pymol-users

[PyMOL] Show sticks till a certain radius

[Horacio E. P. S. <hor...@in...>]

Hi,

Given a receptor in cartoon representation and a ligand (sticks) in its 
cavity, center of mass x, y, z, I wonder how could I get the sticks 
representation of the protein (in addition to cartoon) but only in a 
region limited by a sphere of radius "R", with center at x, y, z.

Thanks in advance

Horacio

Re: [PyMOL] Show sticks till a certain radius

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

Hi Horacio,

Do you really need a sphere around (x,y,z)? That's tough. But I'd
reckon it's more meaningful to select all residues within a certain
distance from any atom of the ligand anyway, which is easy:

show sticks, byres protein within 3.5 of ligand

Without 'byres' only the atoms actually within the 3.5 A distance will
be shown as sticks. The 3.5 approximately corresponds to H-bonding
distance, but of course you can change it to whatever value you like.
If you insist on showing sticks within a sphere around the center of
mass, you can use the 'pseudoatom' command in the >1.0 version of
Pymol to first create an atom placed at the center of mass of the
ligand and show the sticks based on the distance to that atom.

Hope it helps,

Tsjerk

On Fri, Mar 28, 2008 at 9:41 PM, Horacio Emilio Pérez Sánchez
<hor...@in...> wrote:
> Hi,
>
>  Given a receptor in cartoon representation and a ligand (sticks) in its
>  cavity, center of mass x, y, z, I wonder how could I get the sticks
>  representation of the protein (in addition to cartoon) but only in a
>  region limited by a sphere of radius "R", with center at x, y, z.
>
>  Thanks in advance
>
>  Horacio
>
>
>
>
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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

Re: [PyMOL] Show sticks till a certain radius

[DeLano S. <de...@de...>]

pseudoatom tmp, pos=[X, Y, Z]
show sticks, tmp expand R
delete tmp

Working example:

load $TUT/1hpv.pdb
pseudoatom tmp, pos=[10.0, 17.0, -3.0]
show sticks, tmp expand 6
delete tmp

But like Tsjerk says, you might want to do something more like:

delete all
load $TUT/1hpv.pdb
show sticks, byres (organic expand 5)
color yellow, organic and elem c

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Horacio Emilio Pérez Sánchez
> Sent: Friday, March 28, 2008 1:42 PM
> To: pym...@li...
> Subject: [PyMOL] Show sticks till a certain radius
> 
> Hi,
> 
> Given a receptor in cartoon representation and a ligand 
> (sticks) in its cavity, center of mass x, y, z, I wonder how 
> could I get the sticks representation of the protein (in 
> addition to cartoon) but only in a region limited by a sphere 
> of radius "R", with center at x, y, z.
> 
> Thanks in advance
> 
> Horacio
> 
> 
> 
> 
> --------------------------------------------------------------
> -----------
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> It's the best place to buy or sell services for just about 
> anything Open Source.
> http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.n
et/marketplace
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> PyMOL-users mailing list
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