Thanks Bob. The kinemage generated by MolProbity is a good way to
locate H-bond and not only. I guess "hb" in the list of contacts
stands for H-bond, but I'm not quite sure what the other abbreviations
stand for (cc, wc, so, etc.). This is the first time I use MolProbity
and I've seen that you work for the Richardson lab, so could you
please give me some hints on how to use that tool to evaluate the
poses of my ligands (geometries, bulking interactions, etc.), if
that's feasible of course. Are there any overall scores that measure
these properties?
thanks in advance,
Tom
Tom,
The simplest thing to do is just to use the dist command to check the
interactions manually.
dist atom1, atom2
If you have a bunch to look at and the ligands are in the PDB then
MolProbity can do contact analysis so you can pull out Hydrogen bonds
that way.
If no one has a better guess, maybe try 1.7 plus the VDW radii of F
(1.35), Cl (1.8), or S (1.85). Seems like a good guess to me.
Cheers,
-bob
On Sat, Jul 26, 2008 at 2:32 PM, Thomas Evangelidis
<[email protected]> wrote:
Hi Pymol users,
I want to display the polar interactions between some ligands and a
receptor, but I 'm not quite sure if Pymol can do that for F, Cl or S
atoms. There's a tutorial on the wiki that explains how to set the
cutoff distance but that refers only to O and N atoms:
http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts
I was wondering if I can do that by modifying those code snippets. I
would greatly appreciate any help. Also if someone knows the distance
H-bond donor and acceptor for F and Cl atoms please tell me. I know
only the respective distance for S which is 4 A maximum.
thanks,
Tom
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