[3dem] Local Resolution
Reza Khayat
rkhayat at ccny.cuny.edu
Tue Jun 12 08:22:11 PDT 2018
I'm not aware of such plots in X-ray crystallography. I think such plots may eventually make their way into X-ray crystallography, as did the CC1/2 from the FSC curves. They can be plotted on composite omit maps so as to diminish user bias, but I think the same question will persist.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031
________________________________
From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of David DeRosier <derosier at brandeis.edu>
Sent: Tuesday, June 12, 2018 10:34 AM
To: Himes.Benjamin at gmail.com
Cc: 3dem at ncmir.ucsd.edu
Subject: Re: [3dem] Local Resolution
Do the x-ray xtallographers have the same convention?
David
On Jun 12, 2018, at 1:27 AM, Benjamin Himes <himes.benjamin at gmail.com<mailto:himes.benjamin at gmail.com>> wrote:
Hi Jillian & Reza,
The figures in the paper that Mohsen linked to, reflect what seems to be a general consensus - displaying the local resolution on a scale akin to a heat map, with higher temperature colors corresponding to higher temperature factors (lower resolution.)
The scale bar proximal to your map is nice, and I would add that you should probably make sure that this scale reflects the full resolution range examined by your local resolution program of choice. It seems common to see a map where many of the reported resolution values are piled up at one end or the other of this range, which to me at least, seems worrisome.
Just my opinion,
HTH,
Ben
------------------------
Benjamin Himes
cryoEM methods development
Grigorieff lab<https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.hhmi.org_owa_redir.aspx-3FC-3DSbsCefkcbOt75jDyr05lpd3OifVN-5FutmfvnhZrtXS7Bl2i2eOXXVCA..-26URL-3Dhttp-253a-252f-252fgrigoriefflab.janelia.org-252f&d=DwMFAg&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=ZlzYM3QbM_Ak7IiWlFZxVqZ9XhLWg8qyw5HEGnF2Fc4&s=QGRgS4lFpEAbOmfoWNgVDF_fkKaIQYc_1_0uAuAgcjY&e=>, HHMI Janelia Research Campus
cryoSTAC development @ emClarity<https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.hhmi.org_owa_redir.aspx-3FC-3D8yDzXj54yTidMevTB7q5m3liEVwqAZ9LxuXQ4iYOVvtl2i2eOXXVCA..-26URL-3Dhttps-253a-252f-252fgithub.com-252fbHimes-252femClarity-252fwiki&d=DwMFAg&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=ZlzYM3QbM_Ak7IiWlFZxVqZ9XhLWg8qyw5HEGnF2Fc4&s=_iKB8kxXKZBA4kOtCc68V8zht-njykYcJouWA_iSvLA&e=>
-------------------------
On Mon, Jun 11, 2018 at 6:32 PM, <3dem-request at ncmir.ucsd.edu<mailto:3dem-request at ncmir.ucsd.edu>> wrote:
Send 3dem mailing list submissions to
3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>
To subscribe or unsubscribe via the World Wide Web, visit
https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem<https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwMFAg&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=ZlzYM3QbM_Ak7IiWlFZxVqZ9XhLWg8qyw5HEGnF2Fc4&s=CG-gS1Ha_7vfeDQQU_p-aVfJrP5L5Sv2d73_QUtwFn4&e=>
or, via email, send a message with subject or body 'help' to
3dem-request at ncmir.ucsd.edu<mailto:3dem-request at ncmir.ucsd.edu>
You can reach the person managing the list at
3dem-owner at ncmir.ucsd.edu<mailto:3dem-owner at ncmir.ucsd.edu>
When replying, please edit your Subject line so it is more specific
than "Re: Contents of 3dem digest..."
Today's Topics:
1. Local resolution image (Reza Khayat)
2. Re: Local resolution image (Jillian Chase)
3. Re: Local resolution image (Mohsen Kazemi)
----------------------------------------------------------------------
Message: 1
Date: Mon, 11 Jun 2018 20:58:00 +0000
From: Reza Khayat <rkhayat at ccny.cuny.edu<mailto:rkhayat at ccny.cuny.edu>>
To: "CCPEM at JISCMAIL.AC.UK<mailto:CCPEM at JISCMAIL.AC.UK>" <CCPEM at JISCMAIL.AC.UK<mailto:CCPEM at JISCMAIL.AC.UK>>,
"3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>" <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>
Subject: [3dem] Local resolution image
Message-ID: <da6fed29a0fc4c2e871cc544a706bfce at CCNY-MBX2.itcs.ccny.lan<mailto:ce at CCNY-MBX2.itcs.ccny.lan>>
Content-Type: text/plain; charset="us-ascii"
Hi,
Has a standard been established in the field for coloring local resolution maps? If not, are there any suggestions (i.e. FSC resolution is blue, 2x FSC resolution is white, and 4x FSC resolution is red). Thanks.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
Department of Chemistry
City College of New York
85 Saint Nicholas Terrace, CDI 2.318
New York, NY 10031
http://www.khayatlab.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.khayatlab.org_&d=DwMFAg&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=ZlzYM3QbM_Ak7IiWlFZxVqZ9XhLWg8qyw5HEGnF2Fc4&s=MhC_zq6L-9-0SB2Gljf62R6I-DUrdXNlTUrh56uZSoc&e=>
212-650-6070
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20180611/a204eeb5/attachment-0001.html<https://urldefense.proofpoint.com/v2/url?u=http-3A__mail.ncmir.ucsd.edu_pipermail_3dem_attachments_20180611_a204eeb5_attachment-2D0001.html&d=DwMFAg&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=ZlzYM3QbM_Ak7IiWlFZxVqZ9XhLWg8qyw5HEGnF2Fc4&s=HPUWrHA9L-5Z6CH4zzdZ9rrrlcQns1Jm1_nsIY3afQw&e=>>
------------------------------
Message: 2
Date: Mon, 11 Jun 2018 17:55:26 -0400
From: Jillian Chase <jillian.d.chase at gmail.com<mailto:jillian.d.chase at gmail.com>>
To: Reza Khayat <rkhayat at ccny.cuny.edu<mailto:rkhayat at ccny.cuny.edu>>
Cc: "3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>" <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>,
"CCPEM at JISCMAIL.AC.UK<mailto:CCPEM at JISCMAIL.AC.UK>" <CCPEM at JISCMAIL.AC.UK<mailto:CCPEM at JISCMAIL.AC.UK>>
Subject: Re: [3dem] Local resolution image
Message-ID: <FA69B6DA-E4A8-49F3-901A-EDAD8AF9A172 at gmail.com<mailto:FA69B6DA-E4A8-49F3-901A-EDAD8AF9A172 at gmail.com>>
Content-Type: text/plain; charset="us-ascii"
Hi All,
I'm also very curious about this- has any standard been implemented? It would be nice to have a general guideline so reported data is more-or-less equally easy to interpret in various papers.
We are in the process of drafting a manuscript and have gone back and forth about how to show local resolution in an intuitive way. Some areas of our map are better or worse than the global resolution. What we've settled on (for now) is a rainbow color spectrum (Chimera) in which the range spans both above and below our global res and we have included the scale next to our map colored by res and labeled with resolution. Is there a universal standard that the community is moving towards for this or are we approaching it correctly (or as best we can) for now?
Any insight would be very useful.
All the best,
Jillian
Jillian Chase
PhD Candidate, Jeruzalmi Lab
CUNY/CCNY
> On Jun 11, 2018, at 4:58 PM, Reza Khayat <rkhayat at ccny.cuny.edu<mailto:rkhayat at ccny.cuny.edu>> wrote:
>
> Hi,
>
> Has a standard been established in the field for coloring local resolution maps? If not, are there any suggestions (i.e. FSC resolution is blue, 2x FSC resolution is white, and 4x FSC resolution is red). Thanks.
>
> Best wishes,
> Reza
>
> Reza Khayat, PhD
> Assistant Professor
> Department of Chemistry
> City College of New York
> 85 Saint Nicholas Terrace, CDI 2.318
> New York, NY 10031
> http://www.khayatlab.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.khayatlab.org_&d=DwMFAg&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=ZlzYM3QbM_Ak7IiWlFZxVqZ9XhLWg8qyw5HEGnF2Fc4&s=MhC_zq6L-9-0SB2Gljf62R6I-DUrdXNlTUrh56uZSoc&e=>
> 212-650-6070
>
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>
> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem<https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwMFAg&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=ZlzYM3QbM_Ak7IiWlFZxVqZ9XhLWg8qyw5HEGnF2Fc4&s=CG-gS1Ha_7vfeDQQU_p-aVfJrP5L5Sv2d73_QUtwFn4&e=>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20180611/fd80e654/attachment-0001.html<https://urldefense.proofpoint.com/v2/url?u=http-3A__mail.ncmir.ucsd.edu_pipermail_3dem_attachments_20180611_fd80e654_attachment-2D0001.html&d=DwMFAg&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=ZlzYM3QbM_Ak7IiWlFZxVqZ9XhLWg8qyw5HEGnF2Fc4&s=9fG6ti9KLGJpjCS-AglyGyzs8CDZ7E2vSrh07oULjdo&e=>>
------------------------------
Message: 3
Date: Mon, 11 Jun 2018 22:32:22 +0000
From: Mohsen Kazemi <mohsen.kazemi at unimelb.edu.au<mailto:mohsen.kazemi at unimelb.edu.au>>
To: Jillian Chase <jillian.d.chase at gmail.com<mailto:jillian.d.chase at gmail.com>>, Reza Khayat
<rkhayat at ccny.cuny.edu<mailto:rkhayat at ccny.cuny.edu>>
Cc: "3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>" <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>,
"CCPEM at JISCMAIL.AC.UK<mailto:CCPEM at JISCMAIL.AC.UK>" <CCPEM at JISCMAIL.AC.UK<mailto:CCPEM at JISCMAIL.AC.UK>>
Subject: Re: [3dem] Local resolution image
Message-ID:
<SYBPR01MB3692C97AE7C2D9622195A39BC3780 at SYBPR01MB3692.ausprd01.prod.outlook.com<mailto:SYBPR01MB3692C97AE7C2D9622195A39BC3780 at SYBPR01MB3692.ausprd01.prod.outlook.com>>
Content-Type: text/plain; charset="utf-8"
Hi Jillian and Reza,
This paper should have some useful answers for you; https://www.ncbi.nlm.nih.gov/pubmed/29395788<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_pubmed_29395788&d=DwMFAg&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=ZlzYM3QbM_Ak7IiWlFZxVqZ9XhLWg8qyw5HEGnF2Fc4&s=8OXu1dJCrQXhWBeAl37OhicAQTM9DtbDCFIPLBSiZjw&e=>. It introduces a method to calculate local resolution ?MonoRes? by J. Vilas et al (Structure, 2018). They propose a fully automatic and accurate method to determine the local resolution of 3D map. And, the method is available in the Scipion.
Cheers,
Mohsen
--
Mohsen Kazemi, PhD, PEng
Postdoctoral Research Fellow
Department of Biochemistry and Molecular Biology
School of Biomedical Sciences
Faculty of Medicine, Dentistry and Health Sciences
The University of Melbourne
Room 363, David Penington Building (Bio21 Institute), 30 Flemington Rd, Parkville, VIC 3052, Australia
Phone : +61 3 834 40285
Email : mohsen.kazemi at unimelb.edu.au<mailto:mohsen.kazemi at unimelb.edu.au><mailto:mohsen.kazemi at unimelb.edu.au<mailto:mohsen.kazemi at unimelb.edu.au>>
mohsenkazemi20 at gmail.com<mailto:mohsenkazemi20 at gmail.com><mailto:mohsenkazemi20 at gmail.com<mailto:mohsenkazemi20 at gmail.com>>
From: 3dem <3dem-bounces at ncmir.ucsd.edu<mailto:3dem-bounces at ncmir.ucsd.edu>> On Behalf Of Jillian Chase
Sent: Tuesday, June 12, 2018 7:55 AM
To: Reza Khayat <rkhayat at ccny.cuny.edu<mailto:rkhayat at ccny.cuny.edu>>
Cc: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>; CCPEM at JISCMAIL.AC.UK<mailto:CCPEM at JISCMAIL.AC.UK>
Subject: Re: [3dem] Local resolution image
Hi All,
I'm also very curious about this- has any standard been implemented? It would be nice to have a general guideline so reported data is more-or-less equally easy to interpret in various papers.
We are in the process of drafting a manuscript and have gone back and forth about how to show local resolution in an intuitive way. Some areas of our map are better or worse than the global resolution. What we've settled on (for now) is a rainbow color spectrum (Chimera) in which the range spans both above and below our global res and we have included the scale next to our map colored by res and labeled with resolution. Is there a universal standard that the community is moving towards for this or are we approaching it correctly (or as best we can) for now?
Any insight would be very useful.
All the best,
Jillian
Jillian Chase
PhD Candidate, Jeruzalmi Lab
CUNY/CCNY
On Jun 11, 2018, at 4:58 PM, Reza Khayat <rkhayat at ccny.cuny.edu<mailto:rkhayat at ccny.cuny.edu><mailto:rkhayat at ccny.cuny.edu<mailto:rkhayat at ccny.cuny.edu>>> wrote:
Hi,
Has a standard been established in the field for coloring local resolution maps? If not, are there any suggestions (i.e. FSC resolution is blue, 2x FSC resolution is white, and 4x FSC resolution is red). Thanks.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
Department of Chemistry
City College of New York
85 Saint Nicholas Terrace, CDI 2.318
New York, NY 10031
http://www.khayatlab.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.khayatlab.org_&d=DwMFAg&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=ZlzYM3QbM_Ak7IiWlFZxVqZ9XhLWg8qyw5HEGnF2Fc4&s=MhC_zq6L-9-0SB2Gljf62R6I-DUrdXNlTUrh56uZSoc&e=><http://www.khayatlab.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.khayatlab.org_&d=DwMFAg&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=ZlzYM3QbM_Ak7IiWlFZxVqZ9XhLWg8qyw5HEGnF2Fc4&s=MhC_zq6L-9-0SB2Gljf62R6I-DUrdXNlTUrh56uZSoc&e=>>
212-650-6070
_______________________________________________
3dem mailing list
3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu><mailto:3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>
https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem<https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwMFAg&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=ZlzYM3QbM_Ak7IiWlFZxVqZ9XhLWg8qyw5HEGnF2Fc4&s=CG-gS1Ha_7vfeDQQU_p-aVfJrP5L5Sv2d73_QUtwFn4&e=><https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem<https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwMFAg&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=ZlzYM3QbM_Ak7IiWlFZxVqZ9XhLWg8qyw5HEGnF2Fc4&s=CG-gS1Ha_7vfeDQQU_p-aVfJrP5L5Sv2d73_QUtwFn4&e=>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20180611/2f80b1bb/attachment.html<https://urldefense.proofpoint.com/v2/url?u=http-3A__mail.ncmir.ucsd.edu_pipermail_3dem_attachments_20180611_2f80b1bb_attachment.html&d=DwMFAg&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=ZlzYM3QbM_Ak7IiWlFZxVqZ9XhLWg8qyw5HEGnF2Fc4&s=pEa9DCp_LIsLyZURK873fyaqKgTzYb47mttsRZKzU2w&e=>>
------------------------------
Subject: Digest Footer
_______________________________________________
3dem mailing list
3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>
https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem<https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwMFAg&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=ZlzYM3QbM_Ak7IiWlFZxVqZ9XhLWg8qyw5HEGnF2Fc4&s=CG-gS1Ha_7vfeDQQU_p-aVfJrP5L5Sv2d73_QUtwFn4&e=>
------------------------------
End of 3dem Digest, Vol 130, Issue 19
*************************************
_______________________________________________
3dem mailing list
3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>
https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20180612/02915b26/attachment-0001.html>
More information about the 3dem
mailing list