A question just came out from a chemistry teachers workshop:
Can you place a label pointing to an ssbond? They wanted to
make it evident for students where hbonds and ssbonds are.
My question: how do I select a particular (or all) ssbond/hbond ?
The idea is not to select neither of the atoms
Hello, Jaime
I'd say you cannot use labels, but you can use echos with 3D
coordinates. Also, you can draw an arrow pointing to the bond
midpoint.
Regarding selecting bonds, I'm not sure. You really select atoms
always I think. But it makes no difference.
More difficult will be to aim at all
Bob, it seems that connected and connect do not accept ssbond
as a parameter. Would that be too dificult to implement?
e.g. I can do
select all; hbond calculate;
select connected(hbond,cys);
but cannot do
select connected(ssbond,cys);
Hey! I forgot we have
select cystine
Jaime, maybe
Dear users,
JMol has been tightly integrated into the protein alignment program
supporting 3D-superposition and multiple 3D sequence alignments of
peptide chains or even entire multiprotein complexes.
Please evaluate the system by clicking the following demo:
just for reference:
Jmol, not JMol, please!
:)
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
Hi Bob,
I was curious what commands you had in mind to use to morph the model back to
setB? The 'compare' command? 'minimize'? 'translateSelected'?
Thanks,
Wayne
Message: 1
Date: Wed, 13 Apr 2011 14:41:51 -0500
From: Robert Hanson hans...@stolaf.edu
Subject: Re: [Jmol-users] An Old Paper and
According to =?ISO-8859-1?Q?Angel_Herr=E1ez?= angel.herr...@uah.es:
I would suggest something like
select _S and connected(_S)
# this works is there is only one SSbond
set echo myBondOne {selected}
echo -- This is a disulphide bond
select connected(hbond)
# here you will need to work
Jmol, not JMol, please!
I support that, and it is stressed in the website, but -for the
record- actually Will York's JMol vanished into thin air time ago.
There is no way to find it on the web.
--
Benefiting from
You would attach a 3D echo rather than a label.
use a SMARTS search for SS:
Var ssBondAtoms = {*}.find(SMARTS,SS)
Then get those bonds:
Var ssBonds = ssBondAtoms.bonds
Now go through those, pinpointing the centers:
for (Var i = 1; i = ssBonds.length; i++) {
Var bondCenter = ssBonds[i].xyz
I was thinking just a little FOR loop that moves the atoms explicitly in a
linear fashion. Nothing fancier than that. You want the morph command now,
I suppose :)
Bob
On Thu, Apr 14, 2011 at 8:31 AM, Wayne Decatur wdeca...@yahoo.com wrote:
Hi Bob,
I was curious what commands you had in
Dear Jaim,
After dislaying a protein in FirstGlance in Jmol: click More Views,
then Disulfide Bonds: Show All. This also shows cysteines (not in
SS bonds) and labels all cys residues. To see met sulfurs, use Find
and enter sulfur and met.
Please recall that scenes generated in FirstGlance can
exactly.
You should be able to test it using
print write(coord, mol)
and then check the console.
On Thu, Apr 14, 2011 at 5:01 PM, r...@ellerbach.com wrote:
If I have selected just the good atoms of an interesting molecule in a
binding pocket will write file.mol or write coords file.mol give
12 matches
Mail list logo
