[phenixbb] Files generated in Autobuild from simulated annealing runs

Tom Terwilliger terwilliger at lanl.gov
Tue Oct 7 08:23:02 PDT 2008

Hi Rebecca,

I'm sorry this didn't get answered on the phenix_bb! I somehow missed  
it too.

When you run an omit map with

model=mymodel.pdb  omit_box_pdb=mymodel.pdb omit_res_start_list=500  

the autobuild wizard edits mymodel.pdb, setting the occupancies of all  
atoms that are within a box enclosing the atoms in residue 500 of  
mymodel.pdb (plus a 2 A border) to zero.  Then it runs the cycles of  
autobuild you specify (in this case just a SA step), and produces a  
density-modified map (resolve_composite_map.mtz) using the resulting  
model to generate phase information (and keeping the occupancies of  
these atoms at zero). If mydata.mtz contains phase information, that  
is used as well.

The output map is in


and a pseudo-map showing where the OMIT region(s) is(are) located is in


The  file


is actually not really relevant or useful when you are doing OMIT maps  
because it is just one of the intermediate files that are produced.   
In this particular example it will be identical to  
resolve_composite_map.mtz but if you do other types of OMIT maps it  
won't be the same.

I changed the output of the autobuild wizard recently, so you might  
want to upgrade to the 1.3-final version. The end of the log file in  
this case should say:

Summary of model-building for run 1  Tue Oct  7 08:17:30 2008
Files are in the directory:  /net/chevy/raid1/terwill/misc/test/ 

Starting mtz file: /net/chevy/raid1/terwill/misc/test/perfect.mtz
Sequence file: /net/chevy/raid1/terwill/misc/test/seq.dat

Composite omit map is in : /net/chevy/raid1/terwill/misc/test/ 

Boundaries of omit regions are in : /net/chevy/raid1/terwill/misc/test/ 

Which I hope is clearer than earlier output in which the  
overall_best_denmod_map_coeff.mtz file is mentioned but is irrelevant.

I hope that helps!
All the best,
Tom T

On Oct 7, 2008, at 7:19 AM, Page, Rebecca wrote:

> Hi Tom,
> I posted the question on the phenix bb and, when I got no response,  
> shot an email over to Frank von Delft, an old friend, to see if he  
> knew answer.
> He didn’t, but recommended I email you directly and to “ask him to  
> post the answer on the general bb :)”. He also mentioned he hadn’t  
> seen the post on the phenix bb and I would be interested to know if  
> you did not see it either (I received it).
> At any rate, here it goes:
> > I am newcomer to phenix and have a rookie question about the  
> generated
> > files using the phenix.autobuild command. I generated an sa-omit map
> > of my model, omitting the coordinates for a bound ligand (ligand is
> > residue
> > 500):
> >
> > phenix.autobuild data=mydata.mtz model=mymodel.pdb
> > omit_box_pdb=mymodel.pdb omit_res_start_list=500  
> omit_res_end_list=500
> > omit_chain_list=A composite_omit_type=sa_omit
> >
> > The output omit map (resolve_composite_map.mtz) looks great.
> >
> >
> > My question is:
> > What, exactly, is the "overall_best_denmod_map_coeff.mtz" in this  
> case
> > and how is it related, if at all, to the  
> "resolve_composite_map.mtz"?
> Thanks for your help,
> Rebecca
> Rebecca Page
> Brown University

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