[phenixbb] PHENIX.apply_ncs question

[Nathaniel Echols]

On Wed, May 7, 2014 at 12:34 PM, Sun Bingfa <sunbingfa at gmail.com> wrote:

> I've been working on a structure using NCS. When I run the
> phenix.apply_ncs to generate the whole structure using the original one
> chain PDB, it gave me a PDB with same atom number on the other chain.
> For example, I start with chain A and end in chain A and B (B is generated
> by NCS), while the atom number on chain B is just a duplicate of chain A,
> starting from 1. This cause error in the subsequent refinement trials.
>

Refinement with what program?  This is certainly not a problem in
phenix.refine (at least using current code); I just tried it with one of
our tutorial structures.

I'm wondering what program can correct this issue.
>

You can run phenix.pdbtools (also in GUI, of course) on the model with no
additional options, and the output will be renumbered.  We can easily
modify phenix.apply_ncs to do this automatically, of course, but programs
really shouldn't crash on the current output.

-Nat
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