[3dem] 3dem Digest, Vol 151, Issue 33

Sun Mar 22 07:45:11 PDT 2020

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. For an icosahedral map in EMAN2 convention as model #0 and a fit PDB as model #1, in chimera run the command

sym #1 group i,n25r coordinateSystem #0

then when you save #1 as PDB, the BIOMT will be added to the PDB header.

i,n25r is the chimera code for the icosahedral orientation convention used in EMAN2 maps. For cryosparc, you would change this to 222r.

Best,
JTK
--
J T Kaelber, PhD
Director, Rutgers New Jersey CryoEM/CryoET Core Facility
Institute for Quantitative Biomedicine
174 Frelinghuysen Rd
Piscataway, NJ 08854
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Sent: Sunday, March 22, 2020 6:21 AM
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Subject: 3dem Digest, Vol 151, Issue 33

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Today's Topics:

   1. Job openings for facility manager and staff in West China
      Cryo-EM Center, Chengdu, Sichuan, China (???)
   2. Covid19 and cryo-EM (Levy Daniel)
   3. Re: Generate BIOMT (Matthias Wolf)

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Message: 1
Date: Sun, 22 Mar 2020 16:27:25 +0800 (GMT+08:00)
From: ??? <zsu at scu.edu.cn>
To: 3dem at ncmir.ucsd.edu
Subject: [3dem] Job openings for facility manager and staff in West
        China Cryo-EM Center, Chengdu, Sichuan, China
Message-ID: <2fea64e3.3d13.171015a9255.Coremail.zsu at scu.edu.cn>
Content-Type: text/plain; charset="utf-8"

Job openings for facility manager and staff in West China Cryo-EM Center, Chengdu, Sichuan, China

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 (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), and clinical research in West China Hospital including the upcoming BSL3 laboratory (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). 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,
 application staff, and IT support.

1. Facility manager
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.

2. Application staff

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.

3. IT support

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.

How to Apply:

Candidates of interest should e-mail your Cover Letter and CV to Zhaoming Su: zsu at scu.edu.cn. Competitive salary and benefits will be provided and are open to negotiation.

???

Best?

??? ???

???????????????

??????????????????

Zhaoming Su

Professor

The State Key Laboratory of Biotherapy

West China Hospital, Sichuan University
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Message: 2
Date: Sun, 22 Mar 2020 09:22:52 +0000
From: Levy Daniel <Daniel.Levy at curie.fr>
To: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
Subject: [3dem] Covid19 and cryo-EM
Message-ID: <6b599bf94e2f4527bba663bdd82449f4 at curie.fr>
Content-Type: text/plain; charset="iso-8859-1"

Dear All
I apologize for that naive question. I'm not an expert on viruses.
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..
A negative answer will be also helpful, thus we could concentrate on others things
Best wishes
Daniel

Daniel L?vy, phD
Molecular Microscopy of Membranes
Institut Curie
UMR CNRS 168
PSL, Sorbonne Universit?
11 rue P.M.Curie
75005 Paris, France
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

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Message: 3
Date: Sun, 22 Mar 2020 10:20:38 +0000
From: Matthias Wolf <matthias.wolf at oist.jp>
To: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
Subject: Re: [3dem] Generate BIOMT
Message-ID:
        <OSAPR01MB45166DEA8D5619D9877FBF4DECF30 at OSAPR01MB4516.jpnprd01.prod.outlook.com>

Content-Type: text/plain; charset="iso-8859-1"

Hi Elad,

the BIOMT entry contains the transformation matrix with rotation as quaternions in 3x3 matrix format. The 4th column contains the x,y,z translations.

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:

lsq_ex
{first_mol_name}
{second_mol_name}
b1 b427
a1
{return}
MATRIX_NAME
write .LSQ_MATRIX_NAME matrix_b_to_a.mat (3f15.8)

The reference molecule has the identity matrix (all zeroes), so it is not rotated or translated.
The x,y,z translations are on the 4th line.
The origin is (0,0,0).
The tricky part is to get the convention right (signs, order of operations, coord system). This is were checking with O is often helpful.
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.
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.

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.

There are probably easier options in one of the cryo-EM programs, like in EMAN2.

   Matthias

On Fri, Mar 20, 2020 at 5:45 PM Elad Binshtein <eladbi at gmail.com> wrote:

> Hi All,
>
> How can I generate the PDB BIOMT remark for my model?
> I have the NCS coordinate and the map symmetry.
>
> Thanks.
>
> --
> ________________________________
> Elad Binshtein, Ph.D.
> Cryo-EM specialist - Senior Scientist
> Crowe lab - Vanderbilt Vaccine Center (vvc)
> MRB4 Room 11475
> Vanderbilt University Medical Center
> Nashville, TN
> Mobile: +1-615-481-4408
> 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
> E-Mail: eladbi at gmail.com
> twitter @EladBinshtein
> ________________________________
>
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