[chimera-dev] more good points from Ed Boas
pett at cgl.ucsf.edu
Thu May 2 15:02:23 PDT 2002
On Thursday, May 2, 2002, at 02:42 PM, Elaine Meng wrote:
> The email below makes some good points. I can answer that "ligand" etc.
> are surface categories and not atom specs, but it does beg the question
> of why we couldn't make them usable as atom specs.
You can of course use the far more awkward "@/surfaceCategory=ligand" atom
spec. I don't think I have any objection to the emulator trying to
interpret otherwise-unrecognized atom specs as surface categories, but we
should probably discuss the ramifications and alternatives before making
such a change.
> The possible answer to the second item is that so far, we have focused
> more on handling correct PDB files, not various pathological cases.
> However, I am not sure what is supposed to happen in a correct PDB file
> when part of a chain is lacking density (e.g. a chain with residues 1-20
> lacking density for residues in the middle...is there supposed to be a
> TER card in that case?).
> Comments on these issues welcome. Thanks,
There won't be a TER card because there is no chain break. The "long bond"
is actually informative in that it indicates missing data, rather than a
true break. I think the current behavior should be retained, since it is
trivial to remove the long bonds with the "longbond" command.
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