[phenixbb] omit map with twinning?

Pavel Afonine PAfonine at lbl.gov
Wed Feb 17 15:44:45 PST 2010

Hi Kelly,

I think if you compute a map using "Create maps" option in PHENIX GUI 
then twinning should be taken care of automatically (although you cannot 
specify your own twin operator - it is determined internally).

Also you can always compute the omit map by omitting your ligand from 
the PDB file and using this model as input for "Create maps" ?

You can "omit" the ligand by setting its occupancies to zero:

phenix.pdbtools model.pdb occupancies.set=0 selection="chain A and 
resseq 123"

Finally, if you are using 1.5, you can use phenix.refine to compute maps:

phenix.refine model.pdb data.mtz strategy=none 
main.number_of_macro_cycles=1 twin_law="h,-k,l" output.prefix=maps_only


PS> You don't need to have a system administrator rights to to install 
PHENIX: you can always install it locally under your account.

On 2/17/10 1:46 PM, Kelly Daughtry wrote:
> Hello all,
> The omit_map in the new gui (version 1.5) is great, but I can not
> include a twin law when calculating the omit map, thus the result is
> very messy unclear maps. I do not know if 1.6 has the solution or not,
> I am still lobbying our computer guy to upgrade to it...
> Is there a way from the command line i can include the twin law in
> autobuild so I can calculate the omit map, or can I just add it into
> the eff file?
> My other solution has been to use the create maps function with my
> data and pdb with ligand removed.
> This works, giving me a nice Fo-DFc map, but it would be nice to be
> able to show a true omit map for the ligand, as is customary in most
> structure papers I have run across.
> Thanks in advance for any help you can provide!
> 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
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