[phenixbb] Omit map output map files

Manoj saxena mks131 at gmail.com
Sun Nov 15 20:19:51 PST 2015

Thanks Dr. Pavel,

This looks simple.


On Sun, Nov 15, 2015 at 11:49 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

> 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.
> Pavel
> 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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