Hi Smith -
This won't tell you anything about the hydrophobic interaction itself, but if
you want to get the distance between the average positions (like center of
mass, but without mass) of two groups of atoms to use as an "approximate"
distance between the two residues/sidechains/etc., you can try something like
this:
pseudoatom ps1, resi 1 and sidechain
pseudoatom ps2, resi 2 and sidechain
show nb_spheres, ps*
distance d1, ps1, ps2
This will create a pseudoatom<http://www.pymolwiki.org/index.php/Pseudoatom> at
the geometric center of each side chain and use that for the distance
measurement.
This is particularly useful with things like pi-cation stacking, where you want
to measure the distance between approximately parallel planar groups like
arginine guanidinium groups and aromatic rings.
Hope that helps.
Cheers,
Jared
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Jul 8, 2015, at 9:20 PM, Osvaldo Martin
<aloctavo...@gmail.com<mailto:aloctavo...@gmail.com>> wrote:
Hi Smith,
Distances are generally defined for two points (although it is possible to
generalize the idea to higher dimensions). Since residues are 3D objects, there
is not such a thing as THE distance between 2 residues. Being said that, as we
generally model residues as a collection of spheres (atoms) you can define
several distances, for example:
* The distance between the centroids of each residue
* The minimum distance between any two atoms of each residue
* The average distance over all atoms of each residue
* The distance between Ca
* etc…
Depending on your problem one of those distance could be a reasonable proxy for
“hydrophobic interaction”, but maybe you will need to use a more complex model
to solve your problem may be some energy scoring function (AKA forcefield).
I hope this helps.
Cheers,
Osvaldo.
On Wed, Jul 8, 2015 at 9:48 PM, Smith Liu
<smith_liu...@163.com<mailto:smith_liu...@163.com>> wrote:
Dear Osvaldo,
I want to know whether hydrophobic interactions between 2 residues exist, thus
I want know the distance between the 2 residues, rather than the distance
between the atom of each of the 2 residues.
Is any sense and method we measure the distance between 2 residues?
Best regards.
Smith
At 2015-07-09 00:52:32, "Osvaldo Martin"
<aloctavo...@gmail.com<mailto:aloctavo...@gmail.com>> wrote:
Hi Smith,
If you want to measure the distance between two residues (hydrophobic or not)
you could choose and atom from each residue and measure the distance between
those two atoms. Is this what you want to do, or something more complex? Could
you provide more details about your problem?
Cheers,
Osvaldo.
On Wed, Jul 8, 2015 at 12:33 PM, Smith Liu
<smith_liu...@163.com<mailto:smith_liu...@163.com>> wrote:
Dear All,
Pymol has the function to measure the distance betweeen 2 atoms. In addition,
if 2 hydrophobic residues are close enough, there will be hydrophobic
interactions betweem them. But will you please tell me how to measure the
distance between 2 hydrophobic residues by pymol?
Best regards.
Smith
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