[phenixbb] PHENIX.apply_ncs question

Nathaniel Echols nechols at lbl.gov
Wed May 7 12:42:30 PDT 2014

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.

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