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