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Subject:

Re: Bayesian polishing bfactor

From:

Takanori Nakane <[log in to unmask]>

Reply-To:

Takanori Nakane <[log in to unmask]>

Date:

Tue, 26 Mar 2019 22:04:33 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (98 lines)

Hi,

You should fix errors in the defoci first.

Best regards,

Takanori Nakane

On 2019/03/26 22:03, Zhao, Haiyan wrote:
> Thanks for your reply, I had another data set from same sample with 20 degree tilt, I got 4.4 A structure in relion, because preferred sample orientation, I need 40 degree tilt data to get better map.
> Do you think that I put both data sets together and do bayesian polishing or I need do a couple of ctf refinements before bayesian polishing?
> Best wishes,
>   
> Haiyan Zha
> Department of Biochemistry and Molecular Genetics
> Voice: 858-869-3633
> 
> 
> 
> 
> 
> 
> 
> On 3/26/19, 3:34 PM, "Takanori Nakane" <[log in to unmask]> wrote:
> 
>> Hi,
>>
>> At 14 A, there is no point running Polishing (yet) and
>> you cannot reliably fit B factors.
>>
>> If you believe the resolution is limited by the defocus gradient,
>> run several cycles of CtfRefine and Refine3D (see hemagglutinin example
>> in our RELION3 paper) or use tilt-aware CTF estimation programs
>> (e.g. Warp, CTFTILT, GoCTF).
>>
>> Best regards,
>>
>> Takanori Nakane
>>
>> On 2019/03/26 21:30, Zhao, Haiyan wrote:
>>> Because it is a tilt 40 degree data set on K3 detector with 200KV Arctic, so far the resolution is 14A after 3D refinement
>>> Resolution range is default,
>>> Dose rate is 1.34 e-/A2,
>>>
>>>    
>>> Haiyan Zhao
>>> Department of Biochemistry and Molecular Genetics
>>> Voice: 858-869-3633
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 3/26/19, 3:17 PM, "Takanori Nakane" <[log in to unmask]> wrote:
>>>
>>>> Hi,
>>>>
>>>> What is the resolution of your structure?
>>>> What is the resolution range you used to fit B factors?
>>>> What is the dose rate?
>>>>
>>>> Best regards,
>>>>
>>>> Takanori Nakane
>>>>
>>>> On 2019/03/26 20:41, Zhao, Haiyan wrote:
>>>>> I collected a tilt data set, when I run bayesian polishing for all
>>>>> particles, I got the b factor like I attached the pdf file, I don’t know
>>>>> what happened? Any suggestions. Thanks
>>>>>
>>>>> Haiyan Zhao
>>>>>
>>>>> Department of Biochemistry and Molecular Genetics
>>>>>
>>>>> Voice: 858-869-3633
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------
>>>>>
>>>>> To unsubscribe from the CCPEM list, click the following link:
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>>>>>
>>>>
>>
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