<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<style type="text/css" style="display:none;"> P {margin-top:0;margin-bottom:0;} </style>
</head>
<body dir="ltr">
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Elad, I'm going to assume you are doing a capsid based on the lab you're in..this can also be done using Chimera.
<span>For an icosahedral map in EMAN2 convention as model #0 and a fit PDB as model #1, in chimera run the command<br>
</span>
<div><br>
</div>
<div>sym #1 group i,n25r coordinateSystem #0<br>
</div>
<div><br>
</div>
<div>then when you save #1 as PDB, the BIOMT will be added to the PDB header.<br>
</div>
<div><br>
</div>
<span>i,n25r is the chimera code for the icosahedral orientation convention used in EMAN2 maps. For cryosparc, you would change this to 222r.</span></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span><br>
</span></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span>Best,</span></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span>JTK</span></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span><span>--<br>
</span>
<div>J T Kaelber, PhD<br>
</div>
<div>Director, Rutgers New Jersey CryoEM/CryoET Core Facility<br>
</div>
<div>Institute for Quantitative Biomedicine<br>
</div>
<div>174 Frelinghuysen Rd<br>
</div>
<span>Piscataway, NJ 08854</span></span><br>
</div>
<div id="appendonsend"></div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> 3dem <3dem-bounces@ncmir.ucsd.edu> on behalf of 3dem-request@ncmir.ucsd.edu <3dem-request@ncmir.ucsd.edu><br>
<b>Sent:</b> Sunday, March 22, 2020 6:21 AM<br>
<b>To:</b> 3dem@ncmir.ucsd.edu <3dem@ncmir.ucsd.edu><br>
<b>Subject:</b> 3dem Digest, Vol 151, Issue 33</font>
<div> </div>
</div>
<div class="BodyFragment"><font size="2"><span style="font-size:11pt;">
<div class="PlainText">Send 3dem mailing list submissions to<br>
3dem@ncmir.ucsd.edu<br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
<a href="https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.ncmir.ucsd.edu%2Fmailman%2Flistinfo%2F3dem&data=02%7C01%7Cjason.kaelber%40rutgers.edu%7Cc9bcc4a904c747fd3d6a08d7ce4ae7bb%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637204693444069742&sdata=FEozRz5%2FM5OLPQeRQOGsIq0MdRXeiZ4Co2nbOdyU80A%3D&reserved=0">
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.ncmir.ucsd.edu%2Fmailman%2Flistinfo%2F3dem&data=02%7C01%7Cjason.kaelber%40rutgers.edu%7Cc9bcc4a904c747fd3d6a08d7ce4ae7bb%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637204693444069742&sdata=FEozRz5%2FM5OLPQeRQOGsIq0MdRXeiZ4Co2nbOdyU80A%3D&reserved=0</a><br>
or, via email, send a message with subject or body 'help' to<br>
3dem-request@ncmir.ucsd.edu<br>
<br>
You can reach the person managing the list at<br>
3dem-owner@ncmir.ucsd.edu<br>
<br>
When replying, please edit your Subject line so it is more specific<br>
than "Re: Contents of 3dem digest..."<br>
<br>
<br>
Today's Topics:<br>
<br>
1. Job openings for facility manager and staff in West China<br>
Cryo-EM Center, Chengdu, Sichuan, China (???)<br>
2. Covid19 and cryo-EM (Levy Daniel)<br>
3. Re: Generate BIOMT (Matthias Wolf)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Sun, 22 Mar 2020 16:27:25 +0800 (GMT+08:00)<br>
From: ??? <zsu@scu.edu.cn><br>
To: 3dem@ncmir.ucsd.edu<br>
Subject: [3dem] Job openings for facility manager and staff in West<br>
China Cryo-EM Center, Chengdu, Sichuan, China<br>
Message-ID: <2fea64e3.3d13.171015a9255.Coremail.zsu@scu.edu.cn><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Job openings for facility manager and staff in West China Cryo-EM Center, Chengdu, Sichuan, China<br>
<br>
<br>
<br>
<br>
The West China Cryo-EM Center is jointly funded by Sichuan University and West China Hospital in Chengdu, Sichuan, China. The facility aims to provide single particle and tomography supports for fundamental and translational research such as novel drug discovery
and gene therapy in The State Key Laboratory of Biotherapy (<a href="https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsklb.scu.edu.cn%2Ff_summary.html&data=02%7C01%7Cjason.kaelber%40rutgers.edu%7Cc9bcc4a904c747fd3d6a08d7ce4ae7bb%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637204693444079740&sdata=J8QU%2FRgW1UWfsH%2FykFhEXfsbhUDW4a7sYop5yvXbIRU%3D&reserved=0">https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsklb.scu.edu.cn%2Ff_summary.html&data=02%7C01%7Cjason.kaelber%40rutgers.edu%7Cc9bcc4a904c747fd3d6a08d7ce4ae7bb%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637204693444079740&sdata=J8QU%2FRgW1UWfsH%2FykFhEXfsbhUDW4a7sYop5yvXbIRU%3D&reserved=0</a>),
and clinical research in West China Hospital including the upcoming BSL3 laboratory (<a href="https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.wchscu.cn%2FHome.html&data=02%7C01%7Cjason.kaelber%40rutgers.edu%7Cc9bcc4a904c747fd3d6a08d7ce4ae7bb%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637204693444079740&sdata=E0lyjzTdHE8%2Fyvq6PmByMUx5HOLF6rBrHF6ezc58RLo%3D&reserved=0">https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.wchscu.cn%2FHome.html&data=02%7C01%7Cjason.kaelber%40rutgers.edu%7Cc9bcc4a904c747fd3d6a08d7ce4ae7bb%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637204693444079740&sdata=E0lyjzTdHE8%2Fyvq6PmByMUx5HOLF6rBrHF6ezc58RLo%3D&reserved=0</a>).
The Center currently has a 300 kV Titan Krios G3i equipped with K2 BioQuantum and Volta phase plate (the 100th Titan Krios in the world and yes we have the plaque), a 200 kV Talos Arctica G2 equipped with Falcon3 and Volta phase plate, and a 120 kV JEOL-1400
mostly for negative stainings. Sample freezing instruments include two Mark IV Vitrobot and one Leica GP2. For cryo-ET, we currently have a Leica CLEM system, and will acquire a FIB system in the coming year. We currently have openings for facility manager,
<br>
application staff, and IT support.<br>
<br>
<br>
<br>
1. Facility manager<br>
Facility manager is responsible for coordinating the routine schedule of the Cryo-EM Center, such as microscope time scheduling, sample preparation, training arrangement, microscope maintenance, etc. Applicants should have a Ph.D. degree in physics, materials,
biology or a related field of science, extensive experience in Cryo-EM is preferred.<br>
<br>
<br>
<br>
<br>
<br>
2. Application staff<br>
<br>
Application staff is responsible for microscope operations, including daily alignment, data collection, sample preparation, user training, etc. Applicants should have a Ph.D. degree in related areas, experience and skills in Cryo-EM are preferred.
<br>
<br>
<br>
<br>
<br>
<br>
3. IT support<br>
<br>
IT support is responsible for maintaining the computational infrastructure of Cryo-EM Center, including data storage, data processing pipeline setup, data statistics analysis, etc. Applicants should have a master degree or above in related areas, experience
in cryo-EM data processing is preferred.<br>
<br>
<br>
<br>
<br>
<br>
How to Apply:<br>
<br>
Candidates of interest should e-mail your Cover Letter and CV to Zhaoming Su: zsu@scu.edu.cn. Competitive salary and benefits will be provided and are open to negotiation.<br>
<br>
<br>
<br>
<br>
???<br>
<br>
Best?<br>
<br>
<br>
<br>
<br>
??? ???<br>
<br>
???????????????<br>
<br>
??????????????????<br>
<br>
<br>
<br>
<br>
Zhaoming Su<br>
<br>
Professor<br>
<br>
The State Key Laboratory of Biotherapy<br>
<br>
West China Hospital, Sichuan University<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmail.ncmir.ucsd.edu%2Fpipermail%2F3dem%2Fattachments%2F20200322%2F7127e89b%2Fattachment.html&data=02%7C01%7Cjason.kaelber%40rutgers.edu%7Cc9bcc4a904c747fd3d6a08d7ce4ae7bb%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637204693444079740&sdata=G2aUjVgfOI4vkv7CKwhh1ImTDgaDmW7XWPDyjpD6qIc%3D&reserved=0">https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmail.ncmir.ucsd.edu%2Fpipermail%2F3dem%2Fattachments%2F20200322%2F7127e89b%2Fattachment.html&data=02%7C01%7Cjason.kaelber%40rutgers.edu%7Cc9bcc4a904c747fd3d6a08d7ce4ae7bb%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637204693444079740&sdata=G2aUjVgfOI4vkv7CKwhh1ImTDgaDmW7XWPDyjpD6qIc%3D&reserved=0</a>><br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Sun, 22 Mar 2020 09:22:52 +0000<br>
From: Levy Daniel <Daniel.Levy@curie.fr><br>
To: "3dem@ncmir.ucsd.edu" <3dem@ncmir.ucsd.edu><br>
Subject: [3dem] Covid19 and cryo-EM<br>
Message-ID: <6b599bf94e2f4527bba663bdd82449f4@curie.fr><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear All<br>
I apologize for that naive question. I'm not an expert on viruses.<br>
However, I would like to know if there's anything we can do for the researchers working on Covd19. This could be, for example, providing access to microscopes, imaging samples under safe conditions, analyzing images, sharing data, answering questions..<br>
A negative answer will be also helpful, thus we could concentrate on others things<br>
Best wishes<br>
Daniel<br>
<br>
Daniel L?vy, phD<br>
Molecular Microscopy of Membranes<br>
Institut Curie<br>
UMR CNRS 168<br>
PSL, Sorbonne Universit?<br>
11 rue P.M.Curie<br>
75005 Paris, France<br>
<a href="https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fscience.institut-curie.org%2Fresearch%2Fteam-levy&data=02%7C01%7Cjason.kaelber%40rutgers.edu%7Cc9bcc4a904c747fd3d6a08d7ce4ae7bb%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637204693444079740&sdata=JKBrZy9L%2FlM9mIIbZHeoRGyrIMsQfqzm9UgIkouCp0s%3D&reserved=0">https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fscience.institut-curie.org%2Fresearch%2Fteam-levy&data=02%7C01%7Cjason.kaelber%40rutgers.edu%7Cc9bcc4a904c747fd3d6a08d7ce4ae7bb%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637204693444079740&sdata=JKBrZy9L%2FlM9mIIbZHeoRGyrIMsQfqzm9UgIkouCp0s%3D&reserved=0</a><br>
<br>
<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmail.ncmir.ucsd.edu%2Fpipermail%2F3dem%2Fattachments%2F20200322%2F45c12e60%2Fattachment.html&data=02%7C01%7Cjason.kaelber%40rutgers.edu%7Cc9bcc4a904c747fd3d6a08d7ce4ae7bb%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637204693444079740&sdata=rTVyKDZMUpMo3FqmEFanDibiqGraS5ENwuTw7mcyM3o%3D&reserved=0">https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmail.ncmir.ucsd.edu%2Fpipermail%2F3dem%2Fattachments%2F20200322%2F45c12e60%2Fattachment.html&data=02%7C01%7Cjason.kaelber%40rutgers.edu%7Cc9bcc4a904c747fd3d6a08d7ce4ae7bb%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637204693444079740&sdata=rTVyKDZMUpMo3FqmEFanDibiqGraS5ENwuTw7mcyM3o%3D&reserved=0</a>><br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Sun, 22 Mar 2020 10:20:38 +0000<br>
From: Matthias Wolf <matthias.wolf@oist.jp><br>
To: "3dem@ncmir.ucsd.edu" <3dem@ncmir.ucsd.edu><br>
Subject: Re: [3dem] Generate BIOMT<br>
Message-ID:<br>
<OSAPR01MB45166DEA8D5619D9877FBF4DECF30@OSAPR01MB4516.jpnprd01.prod.outlook.com><br>
<br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi Elad,<br>
<br>
the BIOMT entry contains the transformation matrix with rotation as quaternions in 3x3 matrix format. The 4th column contains the x,y,z translations.<br>
<br>
In the classic program O, you can generate the matrix between copies of subunits in any position using the LSQ_EXPLICIT command - for example, to find the matrix for an atom sequence between identical molecules a and b:<br>
<br>
lsq_ex<br>
{first_mol_name}<br>
{second_mol_name}<br>
b1 b427<br>
a1<br>
{return}<br>
MATRIX_NAME<br>
write .LSQ_MATRIX_NAME matrix_b_to_a.mat (3f15.8)<br>
<br>
The reference molecule has the identity matrix (all zeroes), so it is not rotated or translated.<br>
The x,y,z translations are on the 4th line.<br>
The origin is (0,0,0).<br>
The tricky part is to get the convention right (signs, order of operations, coord system). This is were checking with O is often helpful.<br>
You can transfer the O-derived matrix directly to the BIOMT lines, but the x,y,z translations must go into the last column instead.<br>
Cryo-EM reconstructions are typically centered not at the corner like for X-ray unit cells, but in the center of the box - must update the map header accordingly. You can do this with Gerard Kleywegth's program MAPMAN (using option translate), or - easier -
in chimera by changing the origin to center and saving the map.<br>
<br>
The CCP4 program PDBSET is also helpful. It can also invert matrices to generate rotation/translation in opposite direction. Actually, I think you can directly generate the matrices with PDBSET using its SYMGEN option by providing the spacegroup. The matrices
should be in the log file. Of course, if you already have the NCS operators in matrix format, you may use them directly for your BIOMT. Always check in chimera or O or COOT if the transformations are correct.<br>
<br>
There are probably easier options in one of the cryo-EM programs, like in EMAN2.<br>
<br>
Matthias<br>
<br>
<br>
On Fri, Mar 20, 2020 at 5:45 PM Elad Binshtein <eladbi@gmail.com> wrote:<br>
<br>
> Hi All,<br>
><br>
> How can I generate the PDB BIOMT remark for my model?<br>
> I have the NCS coordinate and the map symmetry.<br>
><br>
> Thanks.<br>
><br>
> --<br>
> ________________________________<br>
> Elad Binshtein, Ph.D.<br>
> Cryo-EM specialist - Senior Scientist<br>
> Crowe lab - Vanderbilt Vaccine Center (vvc)<br>
> MRB4 Room 11475<br>
> Vanderbilt University Medical Center<br>
> Nashville, TN<br>
> Mobile: +1-615-481-4408<br>
> <a href="https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.linkedin.com%2Fin%2Felad-binshtein-6bb89428%2F&data=02%7C01%7Cjason.kaelber%40rutgers.edu%7Cc9bcc4a904c747fd3d6a08d7ce4ae7bb%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637204693444079740&sdata=7oSbhOzYgN%2FSSzRXNZniczZPqzZ0uys6wzMVGncFo5A%3D&reserved=0">
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.linkedin.com%2Fin%2Felad-binshtein-6bb89428%2F&data=02%7C01%7Cjason.kaelber%40rutgers.edu%7Cc9bcc4a904c747fd3d6a08d7ce4ae7bb%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637204693444079740&sdata=7oSbhOzYgN%2FSSzRXNZniczZPqzZ0uys6wzMVGncFo5A%3D&reserved=0</a><br>
> E-Mail: eladbi@gmail.com<br>
> twitter @EladBinshtein<br>
> ________________________________<br>
><br>
> ------------------------------<br>
><br>
> To unsubscribe from the CCPEM list, click the following link:<br>
> <a href="https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCPEM%26A%3D1&data=02%7C01%7Cjason.kaelber%40rutgers.edu%7Cc9bcc4a904c747fd3d6a08d7ce4ae7bb%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637204693444079740&sdata=SODIKZiZ6p1qd%2FqawTHBA4CLdj2OWl8iSceCOW0PcqE%3D&reserved=0">
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCPEM%26A%3D1&data=02%7C01%7Cjason.kaelber%40rutgers.edu%7Cc9bcc4a904c747fd3d6a08d7ce4ae7bb%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637204693444079740&sdata=SODIKZiZ6p1qd%2FqawTHBA4CLdj2OWl8iSceCOW0PcqE%3D&reserved=0</a><br>
><br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmail.ncmir.ucsd.edu%2Fpipermail%2F3dem%2Fattachments%2F20200322%2F1f9d3c67%2Fattachment.html&data=02%7C01%7Cjason.kaelber%40rutgers.edu%7Cc9bcc4a904c747fd3d6a08d7ce4ae7bb%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637204693444079740&sdata=YZRsWYDkhfUziNbsy%2FvLeMp7wVwDECjv5Ve80llPNLc%3D&reserved=0">https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmail.ncmir.ucsd.edu%2Fpipermail%2F3dem%2Fattachments%2F20200322%2F1f9d3c67%2Fattachment.html&data=02%7C01%7Cjason.kaelber%40rutgers.edu%7Cc9bcc4a904c747fd3d6a08d7ce4ae7bb%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637204693444079740&sdata=YZRsWYDkhfUziNbsy%2FvLeMp7wVwDECjv5Ve80llPNLc%3D&reserved=0</a>><br>
<br>
------------------------------<br>
<br>
Subject: Digest Footer<br>
<br>
_______________________________________________<br>
3dem mailing list<br>
3dem@ncmir.ucsd.edu<br>
<a href="https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.ncmir.ucsd.edu%2Fmailman%2Flistinfo%2F3dem&data=02%7C01%7Cjason.kaelber%40rutgers.edu%7Cc9bcc4a904c747fd3d6a08d7ce4ae7bb%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637204693444079740&sdata=e5F%2FVybv%2BcsuI0KI91jaZ8FceNDxynwzkdvRBzX2flo%3D&reserved=0">https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.ncmir.ucsd.edu%2Fmailman%2Flistinfo%2F3dem&data=02%7C01%7Cjason.kaelber%40rutgers.edu%7Cc9bcc4a904c747fd3d6a08d7ce4ae7bb%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637204693444079740&sdata=e5F%2FVybv%2BcsuI0KI91jaZ8FceNDxynwzkdvRBzX2flo%3D&reserved=0</a><br>
<br>
<br>
------------------------------<br>
<br>
End of 3dem Digest, Vol 151, Issue 33<br>
*************************************<br>
</div>
</span></font></div>
</body>
</html>