[phenixbb] omit map for protein-DNA complex

Terwilliger, Thomas C terwilliger at lanl.gov
Mon Jul 1 13:51:38 PDT 2013

Hi Wei,

I'm sorry for the trouble!  Normally I would expect the SA-omit map to be take a length time that is more or less proportional to the size of the molecule.  It seems possible that in this case something has failed.  

Here is what I'd suggest:  run a plain refinement run of the exact same PDB file and the exact same data file and make sure it runs.  Then if that works, run a SA-refinement run of the same thing. Then if that works, run a simple omit map, and only do it for a single box (use omit_box_start=1 and end=1 in options).  If that works, do the SA-omit-map for a single box. If that works...try the whole SA-omit map again.  

Presumably somewhere along the line something will fail and that will tell you the problem.  Please let us know if it is anything we can fix!

All the best,
Tom T

On Jul 1, 2013, at 1:18 PM, Wei Shi wrote:

> Hi guys, 
> I've been trying to generate the omit map for a protein-DNA complex structure using Phenix. I don't know why it takes forever to run and didn't seem like to finish at all.... The resolution of the dataset is 3.2A. Omit map type: simulated annealing. Omit region: composite. And, for the corresponding apo-protein structure, the simulated annealing omit map was generated within 2 or 3 hours on the same computer cluster. Let me know whether you have any idea about what might go wrong and whether there is anything I could do.... Thank you so much! 
> Best,
> Wei 
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