Thank you so much for your suggestions, Tom!
It seems that something needs to be fixed in the PDB file I was using. I am not sure how I could edit the PDB file to resolve the problems or other things to do to solve this....
Below is the error message I got when I ran a plain refinement of the same PDB file and data file. I also ran phenix.ready-set of the PDB file using default setting (add hydrogen to model if absent, et al) and generate a updated PDB file and ran refine again, but still got the same error message as below:

Number of atoms with unknown nonbonded energy type symbol: 8

Please edit the PDB file to resolve the problems and/or supply a

CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary.

Also note that phenix.ready-set and phenix.elbow are available for creating restraint definitions (CIF files)

Alternatively, to continue despite this problem use:

stop_for_unknowns= False

Thank you so much!

Best,
Wei

On Mon, Jul 1, 2013 at 4:51 PM, Terwilliger, Thomas C <terwilliger@lanl.gov> wrote:

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

> _______________________________________________
> phenixbb mailing list
> phenixbb@phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________
phenixbb mailing list
phenixbb@phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb