[phenixbb] den refinement with multiple reference files

Jeff Headd jjheadd at lbl.gov
Wed Sep 26 09:14:05 PDT 2012

Hi Andreas,

Currently the DEN implementation in Phenix can only take one input file, so
you'll need to combine all reference chains into one .pdb file. The chain
IDs need to match between the working model and the desired reference for
each chain in the reference model, which is how the matching is handled.

In the future this will be more flexible.


On Wed, Sep 26, 2012 at 9:01 AM, Andreas Förster <docandreas at gmail.com>wrote:

> Dear all,
> I've started DEN refinement on a structure obtained by MR from data
> optimistically going to 3.8A.  There are several chains of two kinds in the
> structure.  High-resolution structures exist for both.  How do I use two
> reference files for DEN refinement, and how do I assign which chain
> corresponds to which reference?  (Currently, I'm using reference_file =
> None.)
> Thanks.
> Andreas
> --
>         Andreas Förster, Research Associate
>         Paul Freemont & Xiaodong Zhang Labs
> Department of Biochemistry, Imperial College London
>             http://www.msf.bio.ic.ac.uk
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