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> 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> 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> 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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