[phenixbb] omit map with twinning?

Nathaniel Echols NEchols at lbl.gov
Wed Feb 17 15:56:48 PST 2010

On Feb 17, 2010, at 3:44 PM, Pavel Afonine wrote:
> I think if you compute a map using "Create maps" option in PHENIX GUI then twinning should be taken care of automatically (although you cannot specify your own twin operator - it is determined internally).
> Also you can always compute the omit map by omitting your ligand from the PDB file and using this model as input for "Create maps" ?

My understanding is that this is considered bad practice, unless simulated annealing is added in to remove leftover phase bias.  It would be better to simply take the last refined model before any ligand was added and use that - but an SA omit map would also be acceptable.  (Experimental density, if you have it, would be even better.)

Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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