Hi,
I also strongly recommend people to deposit unfiltered half maps
to EMDB. Many map validation programs and local weighting/scaling
programs require unfiltered half maps.
In RELION these are called run_half1_class001_unfil.mrc and
run_half2_class001_unfil.mrc.
Of course, if you could also deposit raw data to EMPIAR upon
publication, it is even more beneficial for reproducibility,
method development (machine learning methods need huge datasets)
and education.
Best regards,
Takanori Nakane
On 2019/06/18 8:02, Sjors Scheres wrote:
> Dear all,
>
> I strongly agree with Ed's comment here.
>
> Many different programs implement many different ways of measuring
> "resolution", and even within the same program masks or estimated protein
> mass may vary. This makes the numbers very hard to compare. With locally
> varying resolution estimates the problem is even more complex. The actual
> number we attach to our maps is not so important (beyond giving a general
> impression of the quality of the map, e.g. at 4.5A buiding will be very
> hard; at 3.5A one expects to see many side chains; and at 2.5A most of the
> map should be gorgeous). So, compare maps, not numbers. And to help
> reviewers gain the same insights submit your maps with your paper when it
> goes out for review.
>
> HTH,
> Sjors
>
>
>
>
>
>> 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<http://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]<mailto:[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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