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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