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<p>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. <br>
</p>
<p><br>
</p>
<p>Best wishes,<br>
Reza<br>
</p>
<p><br>
</p>
<div id="Signature">
<div name="divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:; margin:0">
Reza Khayat, PhD
<div>Assistant Professor </div>
<div>City College of New York</div>
<div>Department of Chemistry</div>
<div>New York, NY 10031</div>
</div>
</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> 3dem <3dem-bounces@ncmir.ucsd.edu> on behalf of David DeRosier <derosier@brandeis.edu><br>
<b>Sent:</b> Tuesday, June 12, 2018 10:34 AM<br>
<b>To:</b> Himes.Benjamin@gmail.com<br>
<b>Cc:</b> 3dem@ncmir.ucsd.edu<br>
<b>Subject:</b> Re: [3dem] Local Resolution</font>
<div> </div>
</div>
<div>Do the x-ray xtallographers have the same convention?
<div class="">David<br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Jun 12, 2018, at 1:27 AM, Benjamin Himes <<a href="mailto:himes.benjamin@gmail.com" class="">himes.benjamin@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">
<div class="gmail_default" style="font-size:small">Hi Jillian & Reza,</div>
<div class="gmail_default" style="font-size:small"><br class="">
</div>
<div class="gmail_default" style="font-size:small">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.)</div>
<div class="gmail_default" style="font-size:small"><br class="">
</div>
<div class="gmail_default" style="font-size:small">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.</div>
<div class="gmail_default" style="font-size:small"><br class="">
</div>
<div class="gmail_default" style="font-size:small">Just my opinion,</div>
<div class="gmail_default" style="font-size:small"><br class="">
</div>
<div class="gmail_default" style="font-size:small">HTH,</div>
<div class="gmail_default" style="font-size:small"><br class="">
</div>
<div class="gmail_default" style="font-size:small">Ben</div>
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<div dir="ltr" class="">------------------------<br class="">
<font size="2" face="Tahoma" class=""><span dir="ltr" class="" style="font-size:10pt"><font size="1" class=""><span class="" style="font-size:13px"><font face="Arial" class="">Benjamin Himes</font><font face="Arial" class=""><br class="">
</font><font face="Arial" class=""><br class="">
cryoEM methods development </font><font face="Arial" class=""><br class="">
</font><a href="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=" target="_blank" class=""><font face="Arial" class="">Grigorieff
lab</font></a><font face="Arial" class="">, HHMI Janelia Research Campus</font><font face="Arial" class=""><br class="">
</font><font face="Arial" class=""><br class="">
cryoSTAC development @ </font><a href="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=" target="_blank" class=""><font face="Arial" class="">emClarity</font></a><font face="Arial" class=""><br class="">
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<br class="">
<div class="gmail_quote">On Mon, Jun 11, 2018 at 6:32 PM, <span dir="ltr" class="">
<<a href="mailto:3dem-request@ncmir.ucsd.edu" target="_blank" class="">3dem-request@ncmir.ucsd.edu</a>></span> wrote:<br class="">
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Today's Topics:<br class="">
<br class="">
1. Local resolution image (Reza Khayat)<br class="">
2. Re: Local resolution image (Jillian Chase)<br class="">
3. Re: Local resolution image (Mohsen Kazemi)<br class="">
<br class="">
<br class="">
------------------------------<wbr class="">------------------------------<wbr class="">----------<br class="">
<br class="">
Message: 1<br class="">
Date: Mon, 11 Jun 2018 20:58:00 +0000<br class="">
From: Reza Khayat <<a href="mailto:rkhayat@ccny.cuny.edu" class="">rkhayat@ccny.cuny.edu</a>><br class="">
To: "<a href="mailto:CCPEM@JISCMAIL.AC.UK" class="">CCPEM@JISCMAIL.AC.UK</a>" <<a href="mailto:CCPEM@JISCMAIL.AC.UK" class="">CCPEM@JISCMAIL.AC.UK</a>>,<br class="">
"<a href="mailto:3dem@ncmir.ucsd.edu" class="">3dem@ncmir.ucsd.edu</a>" <<a href="mailto:3dem@ncmir.ucsd.edu" class="">3dem@ncmir.ucsd.edu</a>><br class="">
Subject: [3dem] Local resolution image<br class="">
Message-ID: <<wbr class="">da6fed29a0fc4c2e871cc544a706bf<wbr class=""><a href="mailto:ce@CCNY-MBX2.itcs.ccny.lan" class="">ce@CCNY-MBX2.itcs.ccny.lan</a>><br class="">
Content-Type: text/plain; charset="us-ascii"<br class="">
<br class="">
Hi,<br class="">
<br class="">
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.<br class="">
<br class="">
Best wishes,<br class="">
Reza<br class="">
<br class="">
Reza Khayat, PhD<br class="">
Assistant Professor<br class="">
Department of Chemistry<br class="">
City College of New York<br class="">
85 Saint Nicholas Terrace, CDI 2.318<br class="">
New York, NY 10031<br class="">
<a href="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=" rel="noreferrer" target="_blank" class="">http://www.khayatlab.org/</a><br class="">
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Message: 2<br class="">
Date: Mon, 11 Jun 2018 17:55:26 -0400<br class="">
From: Jillian Chase <<a href="mailto:jillian.d.chase@gmail.com" class="">jillian.d.chase@gmail.com</a>><br class="">
To: Reza Khayat <<a href="mailto:rkhayat@ccny.cuny.edu" class="">rkhayat@ccny.cuny.edu</a>><br class="">
Cc: "<a href="mailto:3dem@ncmir.ucsd.edu" class="">3dem@ncmir.ucsd.edu</a>" <<a href="mailto:3dem@ncmir.ucsd.edu" class="">3dem@ncmir.ucsd.edu</a>>,<br class="">
"<a href="mailto:CCPEM@JISCMAIL.AC.UK" class="">CCPEM@JISCMAIL.AC.UK</a>" <<a href="mailto:CCPEM@JISCMAIL.AC.UK" class="">CCPEM@JISCMAIL.AC.UK</a>><br class="">
Subject: Re: [3dem] Local resolution image<br class="">
Message-ID: <<a href="mailto:FA69B6DA-E4A8-49F3-901A-EDAD8AF9A172@gmail.com" class="">FA69B6DA-E4A8-49F3-901A-<wbr class="">EDAD8AF9A172@gmail.com</a>><br class="">
Content-Type: text/plain; charset="us-ascii"<br class="">
<br class="">
Hi All,<br class="">
<br class="">
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.
<br class="">
<br class="">
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?<br class="">
<br class="">
Any insight would be very useful. <br class="">
<br class="">
All the best,<br class="">
Jillian<br class="">
<br class="">
Jillian Chase <br class="">
PhD Candidate, Jeruzalmi Lab<br class="">
CUNY/CCNY<br class="">
<br class="">
> On Jun 11, 2018, at 4:58 PM, Reza Khayat <<a href="mailto:rkhayat@ccny.cuny.edu" class="">rkhayat@ccny.cuny.edu</a>> wrote:<br class="">
> <br class="">
> Hi,<br class="">
> <br class="">
> 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.<br class="">
> <br class="">
> Best wishes,<br class="">
> Reza<br class="">
> <br class="">
> Reza Khayat, PhD<br class="">
> Assistant Professor<br class="">
> Department of Chemistry<br class="">
> City College of New York<br class="">
> 85 Saint Nicholas Terrace, CDI 2.318<br class="">
> New York, NY 10031<br class="">
> <a href="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=" rel="noreferrer" target="_blank" class="">
http://www.khayatlab.org/</a><br class="">
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> <br class="">
> ______________________________<wbr class="">_________________<br class="">
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------------------------------<br class="">
<br class="">
Message: 3<br class="">
Date: Mon, 11 Jun 2018 22:32:22 +0000<br class="">
From: Mohsen Kazemi <<a href="mailto:mohsen.kazemi@unimelb.edu.au" class="">mohsen.kazemi@unimelb.edu.au</a>><br class="">
To: Jillian Chase <<a href="mailto:jillian.d.chase@gmail.com" class="">jillian.d.chase@gmail.com</a>>, Reza Khayat<br class="">
<<a href="mailto:rkhayat@ccny.cuny.edu" class="">rkhayat@ccny.cuny.edu</a>><br class="">
Cc: "<a href="mailto:3dem@ncmir.ucsd.edu" class="">3dem@ncmir.ucsd.edu</a>" <<a href="mailto:3dem@ncmir.ucsd.edu" class="">3dem@ncmir.ucsd.edu</a>>,<br class="">
"<a href="mailto:CCPEM@JISCMAIL.AC.UK" class="">CCPEM@JISCMAIL.AC.UK</a>" <<a href="mailto:CCPEM@JISCMAIL.AC.UK" class="">CCPEM@JISCMAIL.AC.UK</a>><br class="">
Subject: Re: [3dem] Local resolution image<br class="">
Message-ID:<br class="">
<<a href="mailto:SYBPR01MB3692C97AE7C2D9622195A39BC3780@SYBPR01MB3692.ausprd01.prod.outlook.com" class="">SYBPR01MB3692C97AE7C2D9622195<wbr class="">A39BC3780@SYBPR01MB3692.<wbr class="">ausprd01.prod.outlook.com</a>><br class="">
<br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Hi Jillian and Reza,<br class="">
<br class="">
This paper should have some useful answers for you; <a href="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=" rel="noreferrer" target="_blank" class="">
https://www.ncbi.nlm.nih.gov/<wbr class="">pubmed/29395788</a>. 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.<br class="">
<br class="">
Cheers,<br class="">
Mohsen<br class="">
--<br class="">
Mohsen Kazemi, PhD, PEng<br class="">
Postdoctoral Research Fellow<br class="">
<br class="">
Department of Biochemistry and Molecular Biology<br class="">
School of Biomedical Sciences<br class="">
Faculty of Medicine, Dentistry and Health Sciences<br class="">
The University of Melbourne<br class="">
Room 363, David Penington Building (Bio21 Institute), 30 Flemington Rd, Parkville, VIC 3052, Australia<br class="">
<br class="">
Phone : +61 3 834 40285<br class="">
Email : <a href="mailto:mohsen.kazemi@unimelb.edu.au" class="">mohsen.kazemi@unimelb.edu.au</a><<wbr class="">mailto:<a href="mailto:mohsen.kazemi@unimelb.edu.au" class="">mohsen.kazemi@unimelb.<wbr class="">edu.au</a>><br class="">
<a href="mailto:mohsenkazemi20@gmail.com" class="">mohsenkazemi20@gmail.com</a><<wbr class="">mailto:<a href="mailto:mohsenkazemi20@gmail.com" class="">mohsenkazemi20@gmail.<wbr class="">com</a>><br class="">
<br class="">
From: 3dem <<a href="mailto:3dem-bounces@ncmir.ucsd.edu" class="">3dem-bounces@ncmir.ucsd.edu</a>> On Behalf Of Jillian Chase<br class="">
Sent: Tuesday, June 12, 2018 7:55 AM<br class="">
To: Reza Khayat <<a href="mailto:rkhayat@ccny.cuny.edu" class="">rkhayat@ccny.cuny.edu</a>><br class="">
Cc: <a href="mailto:3dem@ncmir.ucsd.edu" class="">3dem@ncmir.ucsd.edu</a>; <a href="mailto:CCPEM@JISCMAIL.AC.UK" class="">
CCPEM@JISCMAIL.AC.UK</a><br class="">
Subject: Re: [3dem] Local resolution image<br class="">
<br class="">
Hi All,<br class="">
<br class="">
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.<br class="">
<br class="">
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?<br class="">
<br class="">
Any insight would be very useful.<br class="">
<br class="">
All the best,<br class="">
Jillian<br class="">
<br class="">
Jillian Chase<br class="">
PhD Candidate, Jeruzalmi Lab<br class="">
CUNY/CCNY<br class="">
<br class="">
On Jun 11, 2018, at 4:58 PM, Reza Khayat <<a href="mailto:rkhayat@ccny.cuny.edu" class="">rkhayat@ccny.cuny.edu</a><mailto:<a href="mailto:rkhayat@ccny.cuny.edu" class=""><wbr class="">rkhayat@ccny.cuny.edu</a>>> wrote:<br class="">
Hi,<br class="">
<br class="">
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.<br class="">
<br class="">
Best wishes,<br class="">
Reza<br class="">
<br class="">
Reza Khayat, PhD<br class="">
Assistant Professor<br class="">
Department of Chemistry<br class="">
City College of New York<br class="">
85 Saint Nicholas Terrace, CDI 2.318<br class="">
New York, NY 10031<br class="">
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