[phenixbb] question about composite SA_omit map in phenix

Thomas C. Terwilliger terwilliger at lanl.gov
Fri Aug 28 07:59:04 PDT 2009

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
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