[PyMOL] Questions_InterfaceResidues

[arooma m. <aro...@gm...>]

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