[phenixbb] Real space difference maps?

Oliver Clarke olibclarke at gmail.com
Tue Mar 15 11:03:05 PDT 2016

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> 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.
> Pavel
> On 3/15/16 10:25, Oliver Clarke wrote:
>> Hello,
>> 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.
>> Cheers,
>> Oli
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