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<DIV><FONT face=Arial size=2>If I understood well your question, you want to
select atoms around a {x y z}.</FONT></DIV>
<DIV><FONT face=Arial size=2>Under VMD, play with the commands:</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>within, same and exwithin.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>An example: </FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>set number_frames [molinfo top get
numframes]</FONT></DIV>
<DIV><FONT face=Arial size=2>set selection [atomselect top "exwithin 3 of
protein"]</FONT></DIV>
<DIV><FONT face=Arial size=2>for {set i 0} {$i < $number_frames} {incr i}
{</FONT></DIV>
<DIV><FONT face=Arial size=2> $selection frame i</FONT></DIV>
<DIV><FONT face=Arial size=2> $selection update</FONT></DIV>
<DIV><FONT face=Arial size=2> set frame_index($i) [$selection
get index]</FONT></DIV>
<DIV><FONT face=Arial size=2>}</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>This will give the index of the atoms around 3
angst. from protein, excluding protein atoms, for each frame in the loaded
traj., and will save index values of those select atoms to the array
frame_index(). </FONT></DIV>
<DIV><FONT face=Arial size=2></FONT><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Though vmd-list is more suitable to answer this
question, just to show you that vmd is really very flexible ;-)</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Regards</FONT></DIV>
<DIV><FONT face=Arial size=2>N.</FONT></DIV>
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<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=vsrid001@odu.edu href="mailto:vsrid001@odu.edu">VISWANADHA
SRIDHARA</A> </DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">Discussion list for GROMACS users</A>
</DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Saturday, July 02, 2005 1:29
AM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> Re: [gmx-users] Re:
make_ndx</DIV>
<DIV><BR></DIV>
<P>Hi Tsjerk,</P>
<P>Thanks for the advice. Actually I knew how to do using VMD, but I need to
get the index file on a fly( say a trajectory), so its kind of difficult to
get index no.s out in a fly using VMD too. Anyways I will try to use Pymol
too.</P>
<P>Thanks. <BR><BR><FONT style="FONT-SIZE: 9pt" size=2><B>"T.A.Wassenaar"
<<A
href="mailto:T.A.Wassenaar@rug.nl">T.A.Wassenaar@rug.nl</A>></B></FONT><BR><FONT
style="FONT-SIZE: 9pt" size=2>Sent by: <A
href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</A></FONT><BR><FONT
style="FONT-SIZE: 9pt" size=2>07/01/2005 09:29 PM ZE2Please respond
toDiscussion list for GROMACS users </FONT><BR><BR><FONT
style="FONT-SIZE: 9pt" size=2>To</FONT> <FONT style="FONT-SIZE: 9pt"
size=2>Discussion list for GROMACS users
<gmx-users@gromacs.org></FONT><BR><FONT style="FONT-SIZE: 9pt"
size=2>cc</FONT> <BR><FONT style="FONT-SIZE: 9pt" size=2>bcc</FONT>
<BR><FONT style="FONT-SIZE: 9pt" size=2>Subject</FONT> <FONT
style="FONT-SIZE: 9pt" size=2>Re: [gmx-users] Re:
make_ndx</FONT><BR> <BR><BR></P>
<P><FONT face=Monospace,Courier>Hi Sri,<BR></FONT><BR><FONT
face=Monospace,Courier>It is not possible to do this in gromacs. Pymol can
make<BR>such selections, but then you need a script to write an<BR>index file
from a Pymol selection. If you know a bit of<BR>python that shouldn't be too
hard.<BR></FONT><BR><FONT face=Monospace,Courier>Hope it
helps,<BR></FONT><BR><FONT face=Monospace,Courier>Tsjerk<BR></FONT><BR><FONT
face=Monospace,Courier>On Fri, 1 Jul 2005 09:33:36 -0400<BR>VISWANADHA
SRIDHARA <vsrid001@odu.edu> wrote:</FONT><BR><FONT
face=Monospace,Courier>> Hi GMX users,<BR>><BR>> I was wondering
whether there is any option in make_ndx<BR>>to get the index of<BR>> the
atoms(or molecules) as a function of the box<BR>>vectors.<BR>> In other
words, can I get the index of the molecules<BR>>separately which
are<BR>> 1nm spherical radius in a 3nm cube as an
example.(say<BR>>cube's center is the<BR>> sphere's center
too).<BR>><BR>> Thanks in advance,<BR>> Sri<BR>><BR>>
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