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

[vivek sharma]

Thanks a lot everybody for the replies...
it has really saved a lot of time for me...:)


With Thanks,
Vivek

2008/10/6 sobereva <sobjubao at yahoo.com.cn>

> Hi
> It's easy to find centroid of a bunch of residues in
> VMD.
> For example,you want to find centroid of residue 1 5
> 8.
> First,you input "atomselect top {resid 1 5 8}" in
> console of VMD,if "atomselect0" appear,then input
> "measure center atomselect0 weight mass",coordinate of
> centroid will display.
>
> For the second question,in VMD,when you pointing at an
> atom,its coordinate will display in console.
> If you want select an atom by specifying its
> coordinate,in "Selected atoms" text box,you can input
> coordinate range of atoms,e.g. "x>3 and x<4".
>
> -- Lu Tian
>
>
> > Hi Everybody,
> > adding a little to my question, can I view the
> > co-ordinate of an atom by
> > pointing at it using mouse or can I select an atom
> > by specifying its
> > co-ordinate only..?
> > Does any of the tool in chimera, pymol, vmd is
> > having such facility.?
> >
> > 2008/10/6 vivek sharma <viveksharma.iitb at gmail.com>
> >
> > > 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 ?
> > >
> > >
> > > With Thanks,
> > > Vivek
>
>
>
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