[phenixbb] Failed to refine B factors of some residues and ligands

[Dorothee Liebschner]

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 <christianroth034 at gmail.com>
wrote:

> 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 <
> christianroth034 at gmail.com> 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] <
>> tzhou at mail.nih.gov> 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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