[phenixbb] Real space difference maps?
pafonine at lbl.gov
Tue Mar 15 11:20:00 PDT 2016
something I'm not quite sure I understand.. if you can see the ligand in
the difference map you should be able to see it in the original
experimental map too (at appropriate contour level).
It's different from crystallography, I think. In crystallography we
almost always use model phases to compute usual maps, meaning we have to
deal with model bias and other artifacts. In cryo-EM the reconstructed
map is your primary data for atomic modeling. If there is signal you
should be able to see it in this map.
On 3/15/16 12:03, Oliver Clarke wrote:
> Hi Pavel, Thanks! Such maps can definitely be helpful, I calculate
> them quite often - to identify bound ligands it is certainly helpful,
> or to highlight regions of the model that have poor fit to the map,
> similar to their use in crystallography.
> On Tue, Mar 15, 2016 at 12:47 PM, Pavel Afonine <pafonine at lbl.gov
> <mailto:pafonine at lbl.gov>> wrote:
> Hi Oliver,
> why not.. I think we can compute map from model and then subtract
> it from the experimental input map (after scaling them somehow).
> No I did not have that plan because it wasn't clear to me how such
> map can be helpful (especially since we don't do best possible job
> on B factor refinement).
> I will add this option.
> On 3/15/16 10:25, Oliver Clarke wrote:
> is there any possibility of (or current plan for) including
> the capacity in a future PHENIX release to calculate a
> residual map automatically after phenix.real_space refine,
> (i.e. simulating a map from the model incorporating
> corrections for B-factor variation and calculating a
> difference map with the experimental map)? This would be very
> convenient when building into EM maps.
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