[chimera-dev] more good points from Ed Boas

[Eric Pettersen]

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.

--Eric