Hi,
> For question 1 which determines the shell diameter, based on your explanation, I guess it was determined by the box size, right? Because you see, the
> diameter of the particle (Target density) was much smaller than the diameter of the Shell.
It is caused by a spherical 2D mask, whose diameter is specified in the [Mask diameter]
in the [Optimization] tab. Sorry, "particle diameter" was confusing.
Takanori
> Looking forward to getting your comment.
>
> Flemming
>
> ------------------------------------------------------------------------------------------------------------------------------------------------------
> *发件人:* Takanori Nakane <[log in to unmask]>
> *发送时间:* 2020年10月14日 21:02
> *收件人:* Flemming Goery <[log in to unmask]>; [log in to unmask] <[log in to unmask]>
> *主题:* Re: [ccpem] on relion de novo 3D model generation
> Hi,
>
>> 1. Which relion parameter determine the diameter of the shell?
>
> Particle diameter.
>
>> 2. Which factors determine the location of the Target density inside the shell?
>
> How good the centering in AutoPick is.
>
>> 3. Which factors determine why site A in the Shell has stronger density than site C in the Shell?
>
> (Probably) neighboring particles.
>
> You don't have to worry about any of them at this step.
> The quality of the initial model is not important at all, as long as
> it is within the convergence radius of Class3D/Refine3D. So you can ignore
> the issue 1.
>
> First, run Refine3D or Class3D using this map, still using a very large pixel size.
> This is just to bring all particles into a consistent origin.
>
> Then re-extract particles with re-centering (this solves the issue 2).
> Run Refine3D, generate a mask, re-refine using the mask and "use solvent flattened
> FSC: Yes". This solves the issue 3.
>
> Best regards,
>
> Takanori Nakane
>
>> Best wishes,
>>
>> Flemming
>>
>> ------------------------------------------------------------------------------------------------------------------------------------------------------
>>
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