No subject

Mon Dec 14 07:15:52 PST 2009

phenix.autobuild twin_law=3D"-k,-h,-l" data.mtz model.pdb omit.eff
(generated from omit_map autobuild.eff)

AssertionError: Sorry, unknown file or keyword: twin_law=3D-k -h -l
Possibilities... (use 'phenix.autobuild --help all' to get full help):
  rebuild_in_place.rebuild_chain_list=3D-k -h -l
  omit.omit_chain_list=3D-k -h -l
  model_building.consider_main_chain_list=3D-k -h -l

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

Including this in autobuild.eff:

  twinning {
    twin_law =3D -h,k,-l
(I also tried variations on location of lines and within the
refinement parameters and such)


Sorry, unrecognized variable:  twin_law =3D -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 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> wrote:
> Nathan
> Were those examples you computed earlier SA omit? That example looked a l=
ot 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 simulat=
ed annealing is added in to remove leftover phase bias. =A0It would be bett=
er to simply take the last refined model before any ligand was added and us=
e that - but an SA omit map would also be acceptable. =A0(Experimental dens=
ity, if you have it, would be even better.)
> ---------------------------------------------
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
> gpg --keyserver --recv-keys 67BA8D5D
> 8AE2 F2F4 90F7 9640 28BC =A0686F 78FD 6669 67BA 8D5D
> _______________________________________________
> phenixbb mailing list
> phenixbb at

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