[phenixbb] Omit map output map files

Pavel Afonine pafonine at lbl.gov
Sun Nov 15 19:49:52 PST 2015

Hi Manoj,

you can do it this way:

1) remove ligand from PDB file;
2) compute mFo-DFc map. This is your ligand-omit map.

Some would advise to do a round of refinement between steps 1-2 above in 
order to remove "memory from the ligand". I'm not convinced this is 
critical though.


On 11/15/15 12:18, Manoj saxena wrote:
> Greetings,
> I would be very grateful if someone can help
> me to explain in I can get F0-Fc omit maps of a particular
> ligands using Phenix.
> I am trying to generate an omit map
> for the ligands in my protein model using the
> composite omit map GUI feature of phenix version 1.10.1-2155.
> I selected my ligands by using atom selection feature under the
> map options(and in the omit map method I put refine). What map type I 
> should give in the map types
> input to get the F0-Fc maps. Currently I may getting a map
> that look like my 2F0-Fc map that I got after my refinement.
> Also, I have no waters in my model.
> Can we define areas (boxes) around the ligand to generate
> omit map of that particular region to get output  maps with densities
> like Fo-Fc maps.
> So many thanks in advance.
> Regards
> Manoj

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