[phenixbb] omit map with twinning?

Pavel Afonine PAfonine at lbl.gov
Thu Feb 18 10:03:09 PST 2010

Hi Kelly,


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 

This will create the desired maps.

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



*Kick maps:*

"(...) An average kick map (AK map) is computed as following (Gunc(ar et 
al., 2000; Turk, 2007; Praz(nikar 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(i?model)  or 
(2mFobs-DFmodel)exp(i?model) 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)
> 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
> <Francis.Reyes at colorado.edu> 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
>> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>> 8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D
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