Re: [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 <[EMAIL PROTECTED]>

> 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 <[EMAIL PROTECTED]>
> >
> > > 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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Re: [gmx-users] Re: Finding centroid for a bunch of residues

[Michael Hirtz]

Hi Vivek,

> 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.?

In VMD the coordinates of an atom you click on will be shwon in the console
after pressing "0" (zero, not O :) while the OpenGL display is in focus (or
selecting "Query" in the "Mouse" menu.

You can select an atom by giving an appropriate selection under
"Graphics"-"Representations"-"Selected Atoms" - like "x = 1.0 and y = 1.0 and
z = 1.0"...

Best,
  Michael
-- 
http://www.defux.de
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