Hi Mohamed,
The value you get out of the FSC calculation depends somewhat sensitively on the mask you provide. Without knowing the details of what was done, it is difficult to really assess the difference in the metrics you have.
Things to think about:
How did your masks change?
What does the plot of the phases randomised beyond X.X Å tell you?
What algorithms or implementations are being used ( as Takanori pointed out, ResMap is different from Relion is different from sxlocres.py is different from blocres) ?
And as Ed rightly pointed out, there is no substitute for actually looking at the density and assessing what differences are visible. Maybe the higher resolution value is an over-estimation, and the lower resolution one is more representative.
As my supervisor used to say many years ago, “the hardest person to convince should be yourself”, so I suggest you dig into the question and find out what’s happening.
Best Regards,
mike
--------
Mike Strauss
McGill University - Dep’t of Anatomy and Cell Biology
3640 University St.
Strathcona Anatomy Bldg, Rm 144
Montreal, QC H3A 0C7
(514) 398-8084
[log in to unmask]
> On 14. Jun 2019, at 06:22, Egelman, Edward H (ehe2n) <[log in to unmask]> wrote:
>
> But you said this in an earlier message:
> “When I apply post processing in Relion on a refined 3D map, the FSC curve gives 0.3 Angstrom worse resolution than that before post processing.”
>
> So my question was did the map actually get worse?
> Regards,
> Ed
>
>
>
>
> Edward Egelman
> Harrison Distinguished Professor
> Department of Biochemistry and Molecular Genetics
> University of Virginia
> phone: 434-924-8210
> fax: 434-924-5069
> [log in to unmask]
> www.people.virginia.edu/~ehe2n
>
> From: Collaborative Computational Project in Electron cryo-Microscopy <[log in to unmask]> on behalf of Mohamed A Sayed <[log in to unmask]>
> Reply-To: Mohamed A Sayed <[log in to unmask]>
> Date: Friday, June 14, 2019 at 5:09 PM
> To: "[log in to unmask]" <[log in to unmask]>
> Subject: Re: [ccpem] Resolution estimation
>
> Hello
> Sorry just for clarification "get 0.x Ang lower resolution compared to Resmap". I really meant that I got two numbers for the same map. I realize that the map quality itself did not change. Thank you
> Best regards
>
> From: Collaborative Computational Project in Electron cryo-Microscopy <[log in to unmask]> on behalf of Egelman, Edward H (ehe2n) <[log in to unmask]>
> Sent: Friday, June 14, 2019 1:44 AM
> To: [log in to unmask]
> Subject: Re: [ccpem] Resolution estimation
>
> Hi,
> I feel compelled to make a comment. When people say that the map has improved (or worsened) by 0.x Å after doing something, do they ever actually look at the map? Or even the FSC curve? Or are they simply looking at the value where FSC=0.143? I think that the most important thing is actually the appearance of the map, and many experienced people have realized that many things can be done to improve or degrade the FSC without changing the overall appearance of the map.
> Regards,
> Ed
>
>
>
> Edward Egelman
> Harrison Distinguished Professor
> Department of Biochemistry and Molecular Genetics
> University of Virginia
> phone: 434-924-8210
> fax: 434-924-5069
> [log in to unmask]
> www.people.virginia.edu/~ehe2n
>
> From: Collaborative Computational Project in Electron cryo-Microscopy <[log in to unmask]> on behalf of Takanori Nakane <[log in to unmask]>
> Reply-To: Takanori Nakane <[log in to unmask]>
> Date: Friday, June 14, 2019 at 6:32 AM
> To: "[log in to unmask]" <[log in to unmask]>
> Subject: Re: [ccpem] Resolution estimation
>
> Hi,
>
> ResMap and RELION use different algorithms to estimate local resolution.
> They are not necessarily comparable.
> (ResMap tends to be more optimistic in my experience)
>
> > Sorry is there any short anwer for how to make the mask less tight.
>
> Please apply low pass filtering at 15 A and add more soft
> edges in MaskCreate.
>
> Best regards,
>
> Takanori Nakane
>
> On 2019/06/13 23:25, Mohamed A Sayed wrote:
>> Hi Takanori,
>> Thank you for your help. This may answer the FSC curve but even when I use Relion to determine the local resolution on the unfiltered refined 3D model I get 0.4 Ang lower resolution compared to Resmap.
>> I used b-factor from post processing and k2 correction curve.
>> Sorry is there any short anwer for how to make the mask less tight. Thank you
>> ________________________________________
>> From: Takanori Nakane <[log in to unmask]>
>> Sent: Thursday, June 13, 2019 9:44 PM
>> To: Mohamed A Sayed;
>> Subject: Re: [ccpem] Resolution estimation
>> Hi,
>> Probably your mask is too tight and/or sharp.
>> Please look at Note 4.16 of
>> ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/multibody_protocol.pdf.
>> Best regards,
>> Takanori Nakane
>> On 2019/06/13 19:27, Mohamed A Sayed wrote:
>>> Hello,
>>>
>>>
>>> I hope you would please advise on the following:
>>>
>>>
>>> When I apply post processing in Relion on a refined 3D map, the FSC
>>> curve gives 0.3 Angstrom worse resolution than that before post processing.
>>>
>>>
>>> If I use Resmap v 1.95 to estimate the resolution from the
>>> unfiltered half maps of the refined model, the resolution is 0.4 A
>>> better than when I use the resolution estimation from Relion on the same
>>> unfiltered half map.
>>>
>>>
>>> - Which value to believe?
>>>
>>> - How to calculate FSC without post processing ?
>>>
>>> - What caused the post processing to give lower resolution and
>>> resolution estimation to be lower?
>>>
>>> Can you please point out for a source on how to reliably fit a pdb into
>>> an cryo map?
>>>
>>> Thank you very much for your help and time.
>>>
>>>
>>>
>>>
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