[phenixbb] Real space difference maps?

Pavel Afonine pafonine at lbl.gov
Tue Mar 15 11:20:00 PDT 2016

Hi Oliver,

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.
> Cheers,
> Oliver.
> 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.
>     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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