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
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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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
Best,
Wei
On Mon, Jul 1, 2013 at 4:51 PM, Terwilliger, Thomas C
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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (2)
-
Terwilliger, Thomas C -
Wei Shi