[phenixbb] Autobuiold from polyalanine model

Terwilliger, Thomas C terwilliger at lanl.gov
Mon Jul 7 08:22:04 PDT 2014

Hi Jie,

I'm sorry for the trouble with phenix.autobuild. Normally if you specify an input model, an input sequence file, and a data file and say "rebuild_in_place=False" as you did, this should replace the side chains on your model.   Could you possibly send me (off-list) the input files that you used and the full log file and I'll have a look?

All the best,
Tom T

On Jul 4, 2014, at 3:50 PM, Chieh Yin wrote:

> 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,
> Jie
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