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 ca
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 (a
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 regard
2 ways:
On the menu:
Wizard --> Measurement --> click atom 1 --> click atom 2
On the prompt:
distance [selection of atom 1], [selection of atom 2]
Shane Caldwell
McGill University
On Wed, Jul 8, 2015 at 11:33 AM, Smith Liu wrote:
> Dear All,
>
> Pymol has the function to measure the distanc
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
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 regar
