Could you please post it on my behalf
Hi Everyone
I have few basic questions, i would really appreciate if any one could answer
In interfaceResidue script,
def interfaceResidues(cmpx, cA='c. A', cB='c. B', cutoff=1.0,
selName="interface"):
dASA cutoff is *1.0*.
*How to decide this cutoff value? In a few examples I have noticed it
is 0.75 and 2.5. *
*I wonder if residues of the two chains (A and B) should be at a
certain distance from each other like 6 or 8 Angstroms? I think I am
confusing dASA with distance between atoms of the residues.*
my second question is
*Is it possible to get the values dASA of the complex and individual
chains (calculated through the script below) printed into any txt or
excel sheet? *
# get the area of the complete complex
cmd.get_area(tempC, load_b=1)
# copy the areas from the loaded b to the q, field.
cmd.alter(tempC, 'q=b')
# extract the two chains and calc. the new area
# note: the q fields are copied to the new objects
# chA and chB
cmd.extract(chA, tempC + " and (" + cA + ")")
cmd.extract(chB, tempC + " and (" + cB + ")")
cmd.get_area(chA, load_b=1)
cmd.get_area(chB, load_b=1)
My third question is in PyMol GUI, by using Action--preset--protein
interface, are we executing the same ResidueInterface script . If yes,
then why is there a difference in results?
If No, what is the difference in both these functions
I would really appreciate if you please answer these questions
Thank you
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