[phenixbb] Real space difference maps?
pafonine at lbl.gov
Tue Mar 15 11:29:57 PDT 2016
ok, this makes sense! I will add option to output difference map and let
time prove its usefulness!
All the best,
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).
> 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.
> 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
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