[chimera-dev] more good points from Ed Boas

Elaine Meng meng at cgl.ucsf.EDU
Thu May 2 14:42:18 PDT 2002

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.  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,
>From boas at stanford.edu Thu May  2 14:10:18 2002
Date: Thu, 02 May 2002 14:10:13 -0700
To: Elaine Meng <meng at cgl.ucsf.EDU>
From: "F. Edward Boas" <boas at stanford.edu>
Subject: Re: Chimera issues/questions

Hi Elaine,

I wasn't expecting such a quick reply ... thanks!  I have a couple more

* Why can you "surface ligand", but not "select ligand"?

* Automatic chain break detection would be really helpful.  Currently,
Chimera connects all the residues in a chain, even when it's clear from the
bond length that there must be a chain break.

Thank you!

F. Edward Boas                                       Phone: 650-787-1688
P.O. Box 17890                              Email: boas at post.harvard.edu
Stanford, CA 94309                    Web: http://www.stanford.edu/~boas

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