[phenixbb] Omit map output map files

Fischmann, Thierry thierry.fischmann at merck.com
Mon Nov 16 05:11:24 PST 2015

What Pavel describes is how to get a “difference map”. But it is not an “omit map” per the original definition.

The omitted part should never have been part of the model during any refinement step before the omit map is calculated. The purpose is to prevent bias.

If the model has already been refined with a ligand, then the technique of simulated annealing refinement can be used to remove the bias after removing the ligand. This approximates an “omit map” (still one may argue not a real “omit map”, but close enough).


From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Manoj saxena
Sent: Sunday, November 15, 2015 11:20 PM
To: Pavel Afonine
Cc: phenixbb at phenix-online.org
Subject: Re: [phenixbb] Omit map output map files

Thanks Dr. Pavel,

This looks simple.


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


On 11/15/15 12:18, Manoj saxena wrote:

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.


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