Miguel wrote:
why isn't ALY from 1jm4 in the protein set, though it contains the
backbone atoms *.N,*.CA,*.C,*.O
http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=1jm4
select [ALY]/1 and (*.N,*.CA,*.C,*.O)
Jan,
This is failing because the N is coming after the CA in the file.
All normal aminoacids have the sequence ordered N, CA, C, O
ATOM 216 N GLY B 715 ... ATOM 217 CA GLY B 715 ... ATOM 218 C GLY B 715 ... ATOM 219 O GLY B 715 ...
This has the sequence CA,N,C,O HETATM 74 CA ALY A 50 ... HETATM 75 N ALY A 50 ... HETATM 76 C ALY A 50 ... HETATM 77 O ALY A 50 ...
The current mechanism enforces proper ordering when trying to recognize special groups.
I suppose we can change this ... but we need to ensure that we don't break something else.
Let me know what you think.
Hi Miguel, I would prefer if the ordering is done by a distance algorithm protein if bound(*.N,*.CA) & bound(*.CA,C) & bound(*.C,*.O) within group; and this should give less false positive results. Regards, Jan
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