[phenixbb] Failed to refine B factors of some residues and ligands
Pavel Afonine
pafonine at lbl.gov
Tue Nov 15 17:50:14 PST 2016
Hi Christian,
somehow this escaped my attention... so was this solved in the end? If
not please send me files and I will find a solution.
Pavel
On 10/31/16 10:55, Christian Roth wrote:
>
> Not more than 5 I'm afraid. I don't know if it would find the right
> B's using 10 cycles and more, but that also increases the running time
> quite considerably even on some of our faster machines.
>
> Best wishes
>
> Christian
>
>
> Am 31.10.2016 um 16:46 schrieb 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 <mailto: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 <mailto: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 <mailto: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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