Dear Bob and anyone interested in finding via SMARTS strings,
I don't think I am reporting a bug but I am interested if my
interpretation below is correct.
I was puzzled that the method you suggested for finding 6-carbon
aromatic rings,
rings = {all}.find("SMARTS","c1ccccc1", true)
failed to find some rings in 2hil. I believe the problem is that 2hil (a
rough model based on cryo-EM) contains many deep clashes. I suspect that
these are deemed by Jmol to be covalent bonds and mess up the SMARTS
matches. Indeed the above command works with another similar model that
I have (can provide on request) that has no clashes.
In the cases I'm analyzing, the clashes are between chains. There are 18
chains in 2hil, each with 11 6-carbon aromatic rings. Thus 198 rings.
The above command finds only 170 rings.
I believe the following command deletes any 'covalent bonds' perceived
by Jmol to be between chains (e.g. bonds resulting from clashes; there
are no disulfides in this model):
connect (all) (not within(chain, _1)) delete
After this, the above rings command indeed finds 198 rings. Now I am
ready to proceed ... :)
Sincerely, Eric
P.S. that "_1" syntax is very useful!
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