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

sobereva sobjubao at yahoo.com.cn
Mon Oct 6 14:33:46 CEST 2008

It's easy to find centroid of a bunch of residues in
For example,you want to find centroid of residue 1 5
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


More information about the gromacs.org_gmx-users mailing list