[phenixbb] Phenix refine selection within distance

Nathaniel Echols nechols at lbl.gov
Tue Feb 11 11:16:23 PST 2014

On Tue, Feb 11, 2014 at 10:55 AM, Andrew Waight <waight at msg.ucsf.edu> wrote:

>           I am trying select a subsection of my molecule only to run TLS
> refinement on. I want to select all residues within a certain distance from
> a given chain. I am using the selection editor within the Phenix interface
> and can't seem to figure out if Phenix provides this functionality in the
> view/pick selection editor. The Phenix.refine manual describes some "smart"
> selections, but they don't seem to work in the selection box. I have tried
> many variations of.
> within(5, chain 'H')
> To no avail. Is this possible to do in the selection editor? Thanks for
> your help.

Not at present, which is actually a mistake - I meant for this to be
switchable.  The basic problem is that the "smart selections" require the
complete interpretation of geometry restraints, which is not fast enough
for interactive use in most cases.  The graphical selection editor is
cheating by guessing the connectivity from interatomic distances, basically
the same thing that PyMOL does.  But that limits us to a subset of
selection syntax.

I'll see if I can quickly add a preferences setting to toggle the method
used to interpret the model.

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