[phenixbb] question about composite SA_omit map in phenix

Nathaniel Echols NEchols at lbl.gov
Fri Aug 28 10:32:28 PDT 2009


Or using a recent installer from the nightly builds page,  
"phenix.omit_map" launches a GUI for this.

On Aug 28, 2009, at 7:59 AM, Thomas C. Terwilliger wrote:

> Hi Qun,
> Yes, you can make a SA composite omit map with:
>
> phenix.autobuild data=data.mtz model=coords.pdb  
> composite_omit_type=sa_omit
>
> All the best,
> Tom T
>
>>> Hi,
>>> I am using molecular replacement to build a model against a 2.2A
>>> resolution
>>> data set. However, the template model only has 23% sequence  
>>> identity.
>>> First,
>>> I use chainsaw in CCP4i to prune all side chain to be poly-Ala  
>>> except the
>>> identical residues. Then I use AutoMR and rigid body refinement, I  
>>> got
>>> Rfree=50%. The continuous electron density is not bad showing second
>>> structures. However, the model has some out-of-registration  
>>> problem, for
>>> example, two proline are in a alpha-helix. In other words, it has  
>>> model
>>> bias. I want to use composite SA-omit to get a less model bias  
>>> map, not a
>>> simple composite omit map or a SA_omit map ommiting a part of the  
>>> region.
>>> Does someone know who to do this?
>>>
>>> Thanks!
>>>
>>> Qun Wan
>>> postdoc fellow
>>> Case Western Reserve University
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>
>
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-------------------
Nathaniel Echols
Lawrence Berkeley Lab
510-486-5136
NEchols at lbl.gov






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