[phenixbb] phenix.get_cc_mtz_pdb but allow for atom selections.

Nathaniel Echols nechols at lbl.gov
Sat Mar 3 17:18:41 PST 2012

On Sat, Mar 3, 2012 at 8:27 AM, Pavel Afonine <pafonine at lbl.gov> wrote:
> phenix.real_space_correlation
> allows to compute correlations between nearly any user-defined maps, can use
> x-ray or neutron scattering dictionaries, accepts atoms selections, detail
> level (cc per residue, atom etc).

This doesn't let you define your own level of detail, e.g. CC for a
domain, or a loop.  It would need to be refactored to pick out map
grid points corresponding to a user-input atom selection instead of
each residue or each atom.  This could theoretically be done for
get_cc_mtz_pdb, but I think that uses RESOLVE internally to handle the
origin shift, which makes it non-trivial to change.  In this case it
is probably overkill.

> I don't remember if it is available in the GUI (Nat to confirm), if not then
> it would be good to have.

It's not in the GUI because I found it far too confusing - looking at
the code again I am still not sure what some of the parameters mean.
I assume this is because it's written to be flexible enough to handle
two models or two maps in addition to model-vs-map, but this makes it
far too cumbersome for routine use.  The validation GUI includes the
same residue-or-atom enumeration anyway, which is what 99% of users
would use phenix.real_space_correlation for anyway.  What Francis is
asking for is something like this:

phenix.some_awesome_new_command model.pdb data.mtz selection="rename LIG"

which phenix.real_space_correlation cannot do, especially since it
does not seem to be able to figure out what to do with model and data
files automatically.


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