I would like to generate a list of distances between the centers of
aromatic rings, identifying the pair of residues that each distance
represents.
I believe the following reports the center of the 6-carbon ring of Tyr3
in 1pgb:
load =1pgb
select tyr3 and sidechain and not (*.cb, *.oh) # selects 6 carbon atoms
print {selected}.xyz
I suppose the first step is to generate a list of ring-center
coordinates for all rings. How would I do that? (I haven't figured out
how to use 'isaromatic'.)
How could I best identify the residue associated with each ring-center?
Perhaps with another list?
If I had such lists, how would I generate a list of distances between
the ring-centers, being able to identify the two residues for each distance?
-------------------
What I have figured out is how to generate a list of distances between
atoms in aromatic rings:
First I select the atoms in the aromatic ring of e.g. Tyr3, and define
that atom set as thisring.
Next I select the atoms in all aromatic rings excluding Tyr3, and define
that atom set as otherrings.
Next, these two commands write a file containing the inter-atomic
distances, along with the two atoms associated with each distance:
xm = measure({thisring}, {otherrings})
write inline @xm distances.txt
The lines in such a file (not from 1pgb) look like this:
distance 10.18 "10.18 \u00c5" [PHE]137:L.CE2 #2056
[TRP]55:I.CZ3 #1468
distance 9.93 "9.93 \u00c5" [PHE]137:L.CE2 #2056
[TRP]55:I.CH2 #1469
distance 16.34 "16.34 \u00c5" [PHE]137:L.CE2 #2056
[PHE]1:O.CG #1062
The resulting file distances.txt can be imported into Excel and sorted
by distance.
But what I want is such a file for distances between the centers of
aromatic rings, rather than all the atoms in those rings.
Thanks, Eric
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