[phenixbb] Autobuiold from polyalanine model

Chieh Yin xtaler at gmail.com
Fri Jul 4 14:50:07 PDT 2014

Dear Phenix Users,

I am doing the molecular replacement to solve a membrane protein
structure(transmembrane and soluble domain). The structure of the soluble
domain is known, 200AAs. And there is a homology structure of transmembrane
domain, 350AAs. I used the polyalanine model of the homologous model of
transmembrane domain to do the first search.  I got a solution with TFZ 16.
Then used the partial solution to do the second search with the soluble
domain as the model.I also got a solution with TFZ about 15. The density
map showed I got the right solution. And the simple rigid body refinement
yielded a Rfactor/Rfree 0.29/0.32. Then I used the polyalanine model and
the soluble domain as the starting model to do the phenix autobuild. But it
seemed that Autobuild didn't replace the alanine with the real sequence
AAs. I tried to set the rebuild in place to false but I still got the same
result. The Autobuild even didn't change any amino aside reside from the
starting model. I hope you could figure out the problem for me. Thank you
in advance!

Best regards,
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