[gmx-users] Finding centroid for a bunch of residues

[sobereva]

Hi,
You can do that in VMD.
e.g. if you want to select residues lying within 15
angstrom of residue 123,input this in "Selected atom"
textbox:

same residue as {protein within 15 of resid 123}

--Lu Tian

> Hi all experts,
> 
> Can I select all the residue which are lying within
> a given distance from
> one residue ?, using any of the tool in pymol, vmd,
> chimera or gromacs.
> Whether the option of g_hbond which gives the pair
> within a particular
> distance can be used for the same purpose ?, FYI, I
> am having one pdb entry
> for the same (no .trr and .tpr).
> 
> with thanks,
> Vivek
> 
> 2008/10/6 Steven Kirk <steven.kirk at hv.se>
> 
> >
> >  Hi there,
> >>
> >> This is the question out of gromacs..but I need
> it urgently.. and I hope
> >> this is the only place where I can get such
> expert to solve my query...
> >> while trying to restrict my MDRUN for a
> particular site of the protein
> >> molecule I want to visualize the site and find
> out the centroid for the
> >> particular site......
> >>
> >> Is there any visualization tool that can do the
> same ..
> >> I mean Is there any molecular visualization tool
> that can help in finding
> >> out the ...centroid between a group of resuidues
> ?
> >>
> >
> > Pymol has a script that computes the center of
> mass for a selection, and
> > optionally, moves this center of mass to the
> origin:
> >
> > http://pymolwiki.org/index.php/COM
> >
> > Haven't used it myself, so I can't vouch for its
> effectiveness.
> >
> > Steve Kirk
> > --
> > Dr. Steven R. Kirk           <steven.kirk at hv.se,
> S.R.Kirk at physics.org>
> > Dept. of Technology, Mathematics & Computer
> Science  (P)+46 520 223215
> > University West                                   
>   (F)+46 520 223299
> > Trollhattan 461 86 SWEDEN                    
> http://beacon.webhop.org
> >
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