Dear Takanori and all,
the issue is solved: As already reported, during refinement I
received several warning messages like:
----------------------------------------------------
Expectation iteration 14
0.43/1.53 min ................~~(,_,"> WARNING: norm_correction= 36850.2
for particle 80 in group 3; Are your groups large enough? Or is the
reference on the correct greyscale?
1.62/1.62 min
............................................................~~(,_,">
---------------------------------------------------
that I ignored.
When regrouping the particle images in Select and rerunning the
refinement everything worked fine including the curves in the FSC plot.
I obtained a final resolution of 4.3 A, which is much more reasonable
for this data set!
Thanks to all for your input, best, Dieter
------------------------------------------------------------------------
Dieter Blaas,
Max Perutz Laboratories
Medical University of Vienna,
Inst. Med. Biochem., Vienna Biocenter (VBC),
Dr. Bohr Gasse 9/3,
A-1030 Vienna, Austria,
Tel: 0043 1 4277 61630,
Mobile: 0043 699 1942 1659
e-mail: [log in to unmask]
------------------------------------------------------------------------
On 15.02.2021 22:12, Takanori Nakane wrote:
> Hi,
>
> This is strange. You should trust the value from PostProcess.
>
> Refine3D reports the HIGHEST resolution where the FSC
> crosses 0.143 (or 0.5 during iterations), while PostProcess
> reports the LOWEST resolution. If your FSC curve has
> oscillations or bumps, Refine3D can give too high resolution.
>
> Don't you have oscillations in the FSC?
> Did you make sure you don't have duplicated particles?
>
> Best regards,
>
> Takanori Nakane
>
> On 2021/02/15 19:00, Dieter Blaas wrote:
>> Sorry to come back to this issue but is it OK that this value is also
>> output in run.out?
>>
>> .........................
>>
>> Calculating solvent-corrected gold-standard FSC ...
>> + randomize phases beyond: 4.34912 Angstroms
>> Maximization ...
>> 000/??? sec ~~(,_,"> [oo]^M3.08/3.08 mi$
>> Auto-refine: Refinement has converged, stopping now...
>> Auto-refine: + Final reconstruction from all particles is saved as:
>> Refine3D/job030/run_cla$
>> Auto-refine: + Final model parameters are stored in:
>> Refine3D/job030/run_model.star
>> *Auto-refine: + Final data parameters are stored in:
>> Refine3D/job030/run_data.star**
>> ** Auto-refine: + Final resolution (already with masking) is: 1.9804**
>> *---------------------------
>>
>> Best, Dieter
>>
>> ------------------------------------------------------------------------
>> Dieter Blaas,
>> Max Perutz Laboratories
>> Medical University of Vienna,
>> Inst. Med. Biochem., Vienna Biocenter (VBC),
>> Dr. Bohr Gasse 9/3,
>> A-1030 Vienna, Austria,
>> Tel: 0043 1 4277 61630,
>> Mobile: 0043 699 1942 1659
>> e-mail:[log in to unmask]
>> ------------------------------------------------------------------------
>>
>> On 15.02.2021 16:57, Takanori Nakane wrote:
>>> Hi,
>>>
>>> You are looking at wrong items.
>>>
>>> rlnCurrentResolution and rlnCurrentImageSize in model.star's
>>> "model_general" table are those used for alignment and backprojection.
>>> Since "the last iteration will use data to Nyquist frequency",
>>> the value goes up.
>>>
>>> You should look at rlnEstimatedResolution in "model_classes" table.
>>>
>>> Best regards,
>>>
>>> Takanori Nakane
>>>
>>> On 2021/02/15 15:50, Dieter Blaas wrote:
>>>> Hi,
>>>>
>>>> some time ago people reported that Postprocess reported
>>>> erroneous resolution values and distorted FSC curves due to an
>>>> incorrect b-factor determined for single particles (I hope I am
>>>> right here). Is this still the case in the above version of relion?
>>>> I used CtfRefine followed by Polishing and, on re-running the
>>>> refinement with shiny.dat, I get the below output on "cat
>>>> *mod*|grep Curr" reporting a erroneous resolution for the last step
>>>> (i.e.combining the two half maps). Is this error related to the
>>>> above one? Why is it occurring? Did I use wrong parameters? The map
>>>> looks OK but does certainly not have 2 A resolution!
>>>>
>>>> I did not see this problem in another refinement following the same
>>>> procedure....
>>>>
>>>> .................................
>>>>
>>>> _rlnCurrentResolution 3.759407
>>>> _rlnCurrentImageSize 348
>>>> _rlnCurrentResolution 3.759407
>>>> _rlnCurrentImageSize 348
>>>> _rlnCurrentResolution 1.980402
>>>> _rlnCurrentImageSize 450
>>>>
>>>> Thanks, best, Dieter
>>>>
>>>> ------------------------------------------------------------------------
>>>>
>>>> Dieter Blaas,
>>>> Max Perutz Laboratories
>>>> Medical University of Vienna,
>>>> Inst. Med. Biochem., Vienna Biocenter (VBC),
>>>> Dr. Bohr Gasse 9/3,
>>>> A-1030 Vienna, Austria,
>>>> Tel: 0043 1 4277 61630,
>>>> Mobile: 0043 699 1942 1659
>>>> e-mail: [log in to unmask]
>>>> ------------------------------------------------------------------------
>>>>
>>>>
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>>>>
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>>
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