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Hi,
<p>When you set the radius, it should be "<tt>$sel set radius</tt> ...".
Note the dollar sign.
<br>Also, please note that when you select "name C" you select only the
carbon of the peptide bond.
<p>Ran.
<p>Albert Sun wrote:
<blockquote TYPE=CITE>Ran, Thanks. I followed your instructions,
first load a .gro file, then typing comments at TkCon:set sel
[atomselect top "name C"]
<br>sel set radius 0.5 Then screen showed should be "set varName ?newValue?"so
I typedset radius 0.1
<p>It does not change radii of atoms, Even though I reload the .gro file,
still no change on screen. Is there any wrong in the above comments. Thanks!
<br><b><i>Ran Friedman <ran@hemi.tau.ac.il></i></b> wrote:
<blockquote class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">You
should put it in the VMD console.
<p>Alternatively, go to extensions -> tkcon, and enter the set of commands
there. You should always have pairs of commands. First, you select a set
of atoms ("e.g. <tt>set sel [atomselect top "name SG or name SE"] </tt>").
Than, you set the radii.
<p>Also, as John Stone mentioned, you should always load a topology file
(.gro or .pdb) as well as your trajectory.
<p>Hope that helped,
<br>Ran.
<p>Albert Sun wrote:
<blockquote TYPE="CITE">Thanks, Ran,I am using VMD uder Windows.I could
not find where should I startset sel [atomselect top "Name" ]$set sel radius
Is it under Molecule or Graphics or Display? Appreciate you could advise
me. Regards, Albert
<p><b><i>Ran Friedman <ran@hemi.tau.ac.il></i></b> wrote:
<blockquote class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">Dear
Albert,
<p>You can change the radii in VMD. Below as an example for sulphur atoms
in proteins:
<p><tt>set sel [atomselect top "name SG or name SE"]</tt>
<br><tt>$sel set radius 1.775</tt>
<p>The name is the name of the atom in the topology file (in this case,
it's a pdb file).
<p>Ran.
<p>Albert Sun wrote:
<blockquote TYPE="CITE">
<p>Dear users,
<p>I am using VMD to view .trr files from Gromacs, and found that
all atoms appear in the same radius.
<p>I don't know if can change the radius of atoms when view the atoms,
either by Gromacs or by VMD. Appreciate you can advise me.
<p>Many Thanks,
<p>Albert
<p>
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<pre>--
------------------------------------------------------
Ran Friedman
Laser laboratory for fast reactions in biology
Department of biochemistry
Faculty of life sciences
Tel-Aviv university
972-3-6409824
------------------------------------------------------</pre>
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<pre>--
------------------------------------------------------
Ran Friedman
Laser laboratory for fast reactions in biology
Department of biochemistry
Faculty of life sciences
Tel-Aviv university
972-3-6409824
------------------------------------------------------</pre>
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<pre>--
------------------------------------------------------
Ran Friedman
Laser laboratory for fast reactions in biology
Department of biochemistry
Faculty of life sciences
Tel-Aviv university
972-3-6409824
------------------------------------------------------</pre>
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