Hi Christian,
OK, it looks you found a way to prevent the positive density by using
"realistic" starting B values (of the order of that of surrounding protein
atoms).
Did you also try to increase the number of macro-cycles?
Best wishes,
Dorothee
On Mon, Oct 31, 2016 at 9:11 AM, Christian Roth
Hi Dorothee
to answer your questions
The resolution is about 2.0 Ang and the average B around 55. The Bfactor from the ligand was set to the default of 20 by Coot when placing the ligands.
It seems that setting the B-value to the average B of the structure nearly solves the problem (most of the ligand fine, just parts with unusuallly high values). Setting it to a bit higher values 70 for a start and the ligand refines fine. I noticed that in the first macrocycle with and initial factor of 20, the B's are nearly unchanged (20 +- 2) Red diff density appears as expected. In the second cycle The minimizer let the B-factors "explode" to about 200 and that basically is the overkill and it never recovers.
HTH
Cheers
Christian
Am 31.10.2016 um 15:59 schrieb Dorothee Liebschner:
Hi Christian,
Could you answer the following questions:
- what is the resolution of the data set? - what is average B of the protein? - what are the starting B values for the ligand? - did you try lowering starting B for the ligand and repeat the refinement? Is this behavior reproducible with different refinement options?
Best wishes,
Dorothee
On Sun, Oct 30, 2016 at 11:06 AM, Christian Roth < [email protected]> wrote:
Hi Phenix Team,
regarding that ligand issue in this thread, we observed the same with a ligand in one of our structures now. After refinement the ligand is surrounded by pos diff density and the B-Factors are around 200 (way above any useful range in that case).
The cif was generated using elbow and phenix runs with options Real space refinement, TLS on, individual B, and optimizing weights. Nothing crazy.
Could you find a solution for the previous case and give us some tips?
Cheers
Christian
Am 06.09.2016 um 01:44 schrieb Pavel Afonine:
Hi Tongqin,
I second Dorothee's point that we need more information to resolve this problem. If you still have this problem please send me inputs files (data, model, .eff from last refinement, as well as ligand .CIF files if any) and I will look into this once I have files.
Pavel
On 8/31/16 09:29, Dorothee Liebschner wrote:
Hi Tongqin,
It is a bit difficult to diagnose with the information you provided. Could you please answer the following questions?
- Did you also try to reset the B-factors to similar values than neighboring atoms? F.ex. the average B-factor in the model could be 50 A**2, but in the ligand region, it could be lower, let's say 20 A**2. Then the starting value using average B is quite far from the likely B-factor of the ligand.
- What refinement strategy do you apply? How many macro-cycles? Do you use any non-default parameters for B-factor refinement?
- Which Phenix version are you using?
Best wishes,
Dorothee
On Wed, Aug 31, 2016 at 7:12 AM, Zhou, Tongqing (NIH/VRC) [E] < [email protected]> wrote:
Dear All,
I am refining a structure with diffraction to 2.2A resolution and 95 % overall completeness. Now the Rs are at 18% and 23%, respectively. But the program failed to refine B factors for several ligands, atoms had high B factors while showing positive Fo-Fc map around them. Occupancy was set to 1 and I also tried to reset B to mean B of the whole PDB. Any of you seeing this phenomenon? Thanks!
Shown below is HEPES that has high B factor and positive density around it after refinement:
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