No subject


Mon Dec 14 07:15:52 PST 2009


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
<a class="moz-txt-link-rfc2396E" href="mailto:Francis.Reyes at colorado.edu">&lt;Francis.Reyes at colorado.edu&gt;</a> wrote:
  </pre>
  <blockquote type="cite">
    <pre wrap="">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:

    </pre>
    <blockquote type="cite">
      <pre wrap="">My understanding is that this is considered bad practice, unless simulated annealing is added in to remove leftover phase bias. &nbsp;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. &nbsp;(Experimental density, if you have it, would be even better.)
      </pre>
    </blockquote>
    <pre wrap="">---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

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