[phenixbb] omit map for protein-DNA complex
wei.shi118 at gmail.com
Tue Jul 2 09:03:41 PDT 2013
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
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
Also note that phenix.ready-set and phenix.elbow are available for creating
restraint definitions (CIF files)
Alternatively, to continue despite this problem use:
Thank you so much!
On Mon, Jul 1, 2013 at 4:51 PM, Terwilliger, Thomas C
<terwilliger at 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
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