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
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
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
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
6 matches
Mail list logo
