FYI I've seen a similar effect at FSC high-frequencies when using
B-factor refinement in relion v3.1
Cheers,
Joe
On 03/12/2019, 21:08, Minglei Zhao wrote:
> OK. Will report back.
>
> Thanks!
>
> Minglei
>
>> On Dec 3, 2019, at 2:50 PM, Takanori Nakane <[log in to unmask]> wrote:
>>
>> Hi,
>>
>> Interesting.
>>
>>> After CtfRefine (first beam tilt, then anisotropic magnification, then defocus)
>> Can you run Refine3D on outputs from each step to see which one was harmful?
>>
>> Best regards,
>>
>> Takanori Nakane
>>
>> On 2019/12/03 20:33, Minglei Zhao wrote:
>>> Just double checked, no intermediate half maps were used in any post processing.
>>> Minglei
>>>> On Dec 3, 2019, at 2:30 PM, Takanori Nakane <[log in to unmask]> wrote:
>>>>
>>>> Hi,
>>>>
>>>> First of all, is "Relion 3.0 beta" typo of
>>>> RELION 3.1 beta? Otherwise, you should use at least RELION 3.0.8.
>>>>
>>>>> the high frequency signal is abnormal (why?), but the curve still looks
>>>> Probably you used half maps from intermediate iterations in PostProcess.
>>>> Please use the converged half maps and repeat subsequent steps.
>>>>
>>>> Best regards,
>>>>
>>>> Takanori Nakane
>>>>
>>>> On 2019/12/03 20:25, Minglei Zhao wrote:
>>>>> Dear Microscopists,
>>>>> I encountered a weird behavior of FSC for an apoferritin dataset processed using Relion 3.0 beta:
>>>>> After 3D refinement and post process, everything looks good:
>>>>> After CtfRefine (first beam tilt, then anisotropic magnification, then defocus), refined again, and post process, the high frequency signal is abnormal (why?), but the curve still looks OK before 0.7(1/A). Estimated resolution improved a little bit:
>>>>> After Bayesian Polishing, refined again using mask and solvent-flattened FSC, the estimated resolution is 1.9 A, FSC from Refine3D job looks fine:
>>>>> However, using the same mask in the previous refinement to filter and sharpen the map, the FSC curve is messed up:
>>>>> Any obvious things I did wrong?
>>>>> Thanks for your attention.
>>>>> Minglei
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