Hi
You're passing more than one atom per selection to the cmd.distance()
function, in which case the function returns the average between the
measured distances (http://pymolwiki.org/index.php/Distance#PYMOL_API ).
On a side note, this could be done much simpler:
fetch 2nuz, async=0
h_add resn LEU and name CD1+CD2
set distance_exclusion, 4
distance aaaa, hydro, hydro, cutoff=5.0, mode=3
run
https://github.com/Pymol-Scripts/Pymol-script-repo/raw/master/get_raw_distances.py
get_raw_distances aaaa
Cheers,
Julian
On Wed, May 4, 2016 at 11:48 PM, riddhiman sarkar <
riddhiman.sar...@gmail.com> wrote:
> Hello ,
> I am a new Pymol user. I am trying to calculate all the H-H distances
> between the methyl protons (CH3) in different Leucine residues in a
> protein, which are within 5A. For some reason, if I rerun the program with
> a distance threshold of 2A, I get different values for the same atoms. Here
> is the script that I am using. It would be great if someone can let me know
> what I am doing wrong.
> *******************************************
>
> pymol.cmd.load('2nuz.pdb', '2nuz')
> pymol.cmd.disable("all")
> pymol.cmd.enable('2nuz')
>
>
> pymol.cmd.h_add("all")
> select1= '(neighbor 2nuz and resn LEU and (name CD1 or name CD2)) and (not
> elem c)'
> atoms = pymol.cmd.get_model(select1)
> select3= '(neighbor 2nuz and resn LEU'
> select4= ' and (name CD1 or name CD2)) and (not elem c) and name '
>
> for at in atoms.atom:
> x1=str(at.resi)
> v1= select3 + select4 + str(at.name)
> for at2 in atoms.atom:
> x2= str(at2.resi)
> v2= select3 + select4 + str(at2.name)
> if x1== x2:
> break
> elif x1 != x2:
> print
> str(at.resn)+str(at.resi)+'-'+str(at2.resn)+str(at2.resi),str(at.name
> )+'-'+str(at2.name), pymol.cmd.distance('aaaa',v1,v2,2.0)
> pymol.cmd.quit()
> ******************************************
>
> Here I get LEU10-LEU8 H01-H07 2.71310377121 if I use 5A in the distance
> command whereas I get LEU10-LEU8 H01-H07 1.78031635284 if I use 2A.
>
>
> Thanks a lot,
> Regards,
> Riddhiman Sarkar
>
>
>
>
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