Hi Kelly,

step-by-step:

1) Take your current best model and remove the ligand.

2) Run phenix.refine as following:

phenix.refine model.pdb data.mtz ligands.cif simulated_annealing=true twin_law="-h,-k-l"

This will create the desired maps.

Alternatively to SA omit map, you can compute Averaged Kick omit map (see below).

Pavel.

PS:

Kick maps:


"(...) An average kick map (AK map) is computed as following (Gunčar et al., 2000; Turk, 2007; Pražnikar et al., 2009): a large ensemble of structures (several hundreds) is created where the coordinates of each structure from the ensemble are all randomly shaken. The shake amount (rmsd distortion introduced to coordinates) varies from 0 to 1.0 Å. Then for each structure a map is computed ((mFobs-DFmodel)exp(iαmodel)  or (2mFobs-DFmodel)exp(iαmodel) or any other map, for example a ligand-omit map). Finally, all maps are averaged out to produce one averaged kick map. An AK map is expected to have less or no bias, less noise, enhance existing signal and potentially can clear up some initially bad densities. (...)"


On 2/18/10 9:55 AM, Kelly Daughtry wrote: 
Thanks everyone for the fast responses!

Ok, so I have tried all of the suggestions.

1) Generate a refinement..eff file which includes the twin law.

When I run from the gui, I do not believe that phenix is actually
including the twin law. It is not shown as being read in the log file
(but the log file show that the refinement.eff was an input). And the
maps look the same as without the twin law. So, either I am doing
something wrong, or it is not reading the twin law.

>From the command line:
phenix.autobuild twin_law="-k,-h,-l" data.mtz model.pdb omit.eff
(generated from omit_map autobuild.eff)

ERROR:
AssertionError: Sorry, unknown file or keyword: twin_law=-k -h -l
Possibilities... (use 'phenix.autobuild --help all' to get full help):
  rebuild_in_place.rebuild_chain_list=-k -h -l
  omit.omit_chain_list=-k -h -l
  model_building.consider_main_chain_list=-k -h -l

So it seems it doesn't know where to include the twin law.

Including this in autobuild.eff:

  twinning {
    twin_law = -h,k,-l
    }
(I also tried variations on location of lines and within the
refinement parameters and such)

AssertionError:

Sorry, unrecognized variable:  twin_law = -h,k,-l

NOTE: this could just be in the wrong scope. Here is the
scope found: autobuild.twinning.twin_law (input line 28)


I looked into the autobuild log file created when I ran the omit_map
without including a twin law, and I do not see any place where that is
taken into account.

2) Omiting ligand and generating difference map (either in
phenix.refine or in create maps utility)
The maps are great, but I really want a SA omit map.

As Nathaniel Echols pointed out, it seems like bad practice.
I am unsure how the entire community feels on the issue, but I have
been taught that a SA omit map gives you validation of your model
(especially in the case of a lignad).


So, what else can I try? Or what am I doing wrong?

Kelly
*******************************************************
Kelly Daughtry
PhD Candidate
Department of Physiology and Biophysics
Boston University School of Medicine
590 Commonwealth Ave
R 390
Boston MA, 02215
(P) 617-358-5548
*******************************************************



On Thu, Feb 18, 2010 at 8:57 AM, Francis E Reyes
<[email protected]> wrote:
  
Nathan

Were those examples you computed earlier SA omit? That example looked a lot better than what I usually get. Do you have any pseudomerohedral cases?

FR

On Feb 17, 2010, at 4:56 PM, Nathaniel Echols wrote:

    
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.)
      
---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

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