[phenixbb] homology models in sculptor

"Weiergräber, Oliver H." o.h.weiergraeber at fz-juelich.de
Sun Apr 6 02:57:53 PDT 2014


Hello,

I am using phenix.sculptor for modification of a homology model in a challenging case of molecular replacement.
The input model is complete (except at the termini), i.e. it exactly matches the target sequence as defined in the alignment file.
In this scenario, are there any caveats to consider with individual options in sculptor?
Specifically, a quick test seems to indicate that the Schwarzenbacher algorithm for side chain pruning does not work, i.e. not a single atom is removed from the model, whereas the alternative "similarity" option leads to deletion of a few hundred atoms.
I'm using sculptor from the command line, and the log file indicates my input is interpreted correctly.

Best regards
Oliver


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  PD Dr. Oliver H. Weiergräber
  Institute of Complex Systems
  ICS-6: Structural Biochemistry
  Tel.: +49 2461 61-2028
  Fax: +49 2461 61-9540
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