VMD-L Mailing List

From: Bassam Haddad (bhaddad_at_pdx.edu)
Date: Sun Mar 01 2020 - 12:09:38 CST

You could also just loop through every pair-wise interaction between all CA
atoms, then save the largest and smallest values. Don’t forget to keep
track of the atom-ID that contributes to the measurement in question.

On Sun, Mar 1, 2020 at 9:49 AM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> The values returned by minmax are explained here:
> http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.3/ug/node138.html
>
> So this will only give you the "maximum" diameter, I think. Perhaps you
> can look into a distribution of atom distances from its center, using the
> g(r) plugin?
>
> On Sun, Mar 1, 2020 at 10:10 AM Yogesh Sharma <yogesh.rma13_at_gmail.com>
> wrote:
>
>> hi,
>> I have a basic question.
>> I am trying to get minimum and maximum diameter of a asymmetric molecule
>> from its pdb file? is it possible to calculate it using minmax command and
>> if it is can you please explain what does the {X, Y ,Z} values in output
>> indicate?
>>
>>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Research collaborator, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
>