[phenixbb] full omit maps

[Jianghai Zhu]

Is this map a total OMIT map like SFCHECK does or a SA-OMIT map like  
CNS does?

Jianghai


On Dec 29, 2006, at 12:53 PM, Thomas C. Terwilliger wrote:

> Hi Miguel,
>
> I'm sorry to have given incorrect instructions!  Here is a corrected
> version of how to make a composite omit map with no rebuilding or
> refinement in phenix (I just did this to be sure).
>
> If you use a script, add the following lines to your rebuild script:
>
>  rebuild_in_place True       # rebuild existing model...
>  rebuild_res_start_list 0    # rebuild only residues 0 to -1 (i.e.,  
> nothing)
>  rebuild_res_end_list -1
>  refine False                # don't refine input model
>  n_cycle_rebuild_min 1       # just do one cycle
>  n_cycle_rebuild_max 1
>
> If you run from a GUI (I didn't test this, but it should work), set  
> the
> same parameters above to these values and it should give you the  
> omit map.
>
> If you just get the overall_best.pdb_OMIT_REGION_1 files then it isn't
> working...if you also get overall_best.mtz_OMIT_REGION_1 then it  
> is.  The
> final map should be resolve_composite_map.mtz. It is produced after  
> all
> the omit region maps are made
>
> Let me know if this doesn't solve the problem!
> All the best,
>
> -Tom T
>
>
>> -----BEGIN PGP SIGNED MESSAGE-----
>> Hash: SHA1
>>
>> Hello everyone,
>>
>> I'm trying to obtain a full omit map as it was described by Tom
>> Terwilliger in a previous post:
>>
>> http://www.phenix-online.org/pipermail/phenixbb/2006-October/ 
>> 000108.html
>>
>> However, when I run the AutoBuild strategy asking for no  
>> rebuilding / no
>> refinement all I get in the FULL_OMIT directory is a collection of  
>> pdb
>> files named 'overall_best.pdb_OMIT_REGION_x' where 'x' correspond to
>> each of the 'omit regions'. But I get no 'resolve_composite_map.mtz'
>> whatsoever.
>>
>> Surely I'm missing something. I would appreciate your guidance.
>>
>> Have all of you an excellent year 2007!
>> All the best,
>>
>>
>> Miguel
>> - --
>> Miguel Ortiz Lombardía
>> Centro de Investigaciones Oncológicas
>> C/ Melchor Fernández Almagro, 3
>> 28029 Madrid, Spain
>> Tel. +34 912 246 900
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20061229/d09980b3/attachment-0004.htm>