[3dem] [ccpem] Resolution estimation
Carlos Oscar S. Sorzano
coss at cnb.csic.es
Sun Jun 16 04:32:52 PDT 2019
Dear all,
we have also seen very often these disagreeing measurements of
resolution depending on the mask being used. In our experience, MonoRes
tends to provide a number that is less biased than other measures. To
use MonoRes you need either two half maps (the preferred option) or a
map and a mask (outside this mask there should be noise that is supposed
to be of the same nature as the noise inside the mask).
Kind regards, Carlos Oscar
El 14/06/2019 a las 11:09, Mohamed A Sayed escribió:
>
> 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 <CCPEM at JISCMAIL.AC.UK> on behalf of Egelman, Edward H
> (ehe2n) <egelman at VIRGINIA.EDU>
> *Sent:* Friday, June 14, 2019 1:44 AM
> *To:* CCPEM at JISCMAIL.AC.UK
> *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
>
> egelman at virginia.edu
>
> www.people.virginia.edu/~ehe2n <http://www.people.virginia.edu/~ehe2n>
>
> *From: *Collaborative Computational Project in Electron
> cryo-Microscopy <CCPEM at JISCMAIL.AC.UK> on behalf of Takanori Nakane
> <tnakane at MRC-LMB.CAM.AC.UK>
> *Reply-To: *Takanori Nakane <tnakane at MRC-LMB.CAM.AC.UK>
> *Date: *Friday, June 14, 2019 at 6:32 AM
> *To: *"CCPEM at JISCMAIL.AC.UK" <CCPEM at JISCMAIL.AC.UK>
> *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 <tnakane at mrc-lmb.cam.ac.uk
> <mailto:tnakane at mrc-lmb.cam.ac.uk>>
>
> 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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--
------------------------------------------------------------------------
Carlos Oscar Sánchez Sorzano e-mail: coss at cnb.csic.es
Biocomputing unit http://i2pc.es/coss
National Center of Biotechnology (CSIC)
c/Darwin, 3
Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510
28049 MADRID (SPAIN) Fax: 34-91-585 4506
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