[phenixbb] Real space difference maps?

[Pavel Afonine]

Hi Oliver,

ok, this makes sense! I will add option to output difference map and let 
time prove its usefulness!

All the best,
Pavel

On 3/15/16 12:26, Oliver Clarke wrote:
> Hi Pavel,
>
> Yes, you can see it in the original map, of course, but it is still 
> useful as a visual aid while building, and to do rigid body fitting of 
> ligands into the difference density (where otherwise they might stray 
> into the protein density at low resolution).
>
> Cheers,
> Oli
>
> On Tue, Mar 15, 2016 at 2:20 PM, Pavel Afonine <pafonine at lbl.gov 
> <mailto:pafonine at lbl.gov>> wrote:
>
>     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.
>
>     Pavel
>
>
>     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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