[phenixbb] HETATM automated chain assignment

Nathaniel Echols nechols at lbl.gov
Fri Feb 15 08:51:55 PST 2013

On Fri, Feb 15, 2013 at 8:39 AM, R.D. Oeffner <rdo20 at cam.ac.uk> wrote:
> In the Phenix GUI under model tools, the program "Sort hetero atom groups"
> shopuld do what you want. You may have to enable alpha-test programs in the
> GUI preferences setttings.

Also available on the command line as "phenix.sort_hetams".  You will
need the latest nightly build for this (1.8.1 doesn't have it), and
Rob is correct that you need to enable alpha-test features (but I'm
changing that now).

There is one potential flaw in the method that I only realized
yesterday, which is that covalently bound HETATMs such as carbohydrate
groups will be treated as free ligands unless they are already part of
a contiguous protein chain (i.e. the chain IDs are the same and there
are no TER records or other atoms intervening in the PDB file).  In
the future we need to take connectivity into account.  However, for
now you can specify an atom selection to be left unmodified if you


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