<DIV>Ran, Thanks.</DIV>
<DIV> </DIV>
<DIV>I followed your instructions, first load a .gro file, then typing comments at TkCon:</DIV>
<DIV>set sel [atomselect top "name C"]<BR>sel set radius 0.5</DIV>
<DIV> </DIV>
<DIV>Then screen showed</DIV>
<DIV> </DIV>
<DIV>should be "set varName ?newValue?"<BR></DIV>
<DIV>so I typed </DIV>
<DIV>set radius 0.1 <BR><BR>It does not change radii of atoms, Even though I reload the .gro file, still no change on screen.</DIV>
<DIV> </DIV>
<DIV>Is there any wrong in the above comments.</DIV>
<DIV> </DIV>
<DIV>Thanks!</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV><BR><B><I>Ran Friedman <ran@hemi.tau.ac.il></I></B> wrote:</DIV>
<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>
<HR SIZE=1>
Do you Yahoo!? <BR><A href="http://antispam.yahoo.com/whatsnewfree">Protect your identity with Yahoo! Mail AddressGuard</A></BLOCKQUOTE><PRE>--
------------------------------------------------------
Ran Friedman
Laser laboratory for fast reactions in biology
Department of biochemistry
Faculty of life sciences
Tel-Aviv university
972-3-6409824
------------------------------------------------------</PRE> </BLOCKQUOTE>
<HR SIZE=1>
Do you Yahoo!? <BR><A href="http://antispam.yahoo.com/whatsnewfree">Protect your identity with Yahoo! Mail AddressGuard</A></BLOCKQUOTE><PRE>--
------------------------------------------------------
Ran Friedman
Laser laboratory for fast reactions in biology
Department of biochemistry
Faculty of life sciences
Tel-Aviv university
972-3-6409824
------------------------------------------------------</PRE> </BLOCKQUOTE><p><hr SIZE=1>
Do you Yahoo!?<br>
<a href="http://antispam.yahoo.com/whatsnewfree">Protect your identity with Yahoo! Mail AddressGuard</a>