Re: [ccp4bb] Figure of merit in refinement

[Andre LB Ambrosio]

Dear Jonathan, many thanks for this. I will have a look at it right away.
With best wishes,
Andre.

On Wed, Oct 2, 2019, 7:51 PM Jonathan Cooper  wrote:

> This is a very good place to start:
>
> https://www-structmed.cimr.cam.ac.uk/Course/Statistics/statistics.html
>
> Also recommend this one:
>
> https://doi.org/10.1107/S0108767386099622
>
> and Main, P. (1979) Acta Cryst. A35, 779-85 - the maths in this one are a
> bit easier!
>
>
>
> On Wednesday, 2 October 2019, 22:47:56 BST, Andre LB Ambrosio <
> an...@ifsc.usp.br> wrote:
>
>
> Dear all,
>
> How is the phase error estimated for any given reflection, specifically in
> the context of model refinement? In terms of math I mean.
>
> How useful is FOM in assessing the phase quality, when not for initial
> experimental phases?
>
> Many thank in advance,
>
> Andre.
>
> --
>
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Re: [ccp4bb] Figure of merit in refinement

[Jonathan Cooper]

 This is a very good place to start:
https://www-structmed.cimr.cam.ac.uk/Course/Statistics/statistics.html

Also recommend this one:
https://doi.org/10.1107/S0108767386099622

and Main, P. (1979) Acta Cryst. A35, 779-85 - the maths in this one are a bit 
easier!


On Wednesday, 2 October 2019, 22:47:56 BST, Andre LB Ambrosio 
 wrote:  
 
 Dear all,
How is the phase error estimated for any given reflection, specifically in the 
context of model refinement? In terms of math I mean.
How useful is FOM in assessing the phase quality, when not for initial 
experimental phases?
Many thank in advance,
Andre.

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[ccp4bb] Figure of merit in refinement

[Andre LB Ambrosio]

Dear all,

How is the phase error estimated for any given reflection, specifically in
the context of model refinement? In terms of math I mean.

How useful is FOM in assessing the phase quality, when not for initial
experimental phases?

Many thank in advance,

Andre.



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[ccp4bb] PhD position in the Chakrabarti group at Freie Universität Berlin, Germany

[Sutapa Chakrabarti]

3-year PhD position at the Freie Universität Berlin

Dear All,

A funded PhD position is available in the lab of Sutapa Chakrabarti (at the 
Institute of Chemistry and Biochemistry, Freie Universität Berlin, Germany) to 
work on  the coupling of mRNA decay and translational repression in eukaryotes 
using structural and biochemical tools. The Chakrabarti lab focuses on 
molecular mechanisms of mRNA decay, particularly  RNA helicases involved in 
decay and  the architecture and assembly of decay competent mRNPs. This 
particular project offers the possibility of exciting collaborations within the 
scope of the German Research Foundation's (DFG) Priority program SPP 1935: 
Deciphering the mRNP code - RNA bound determinants of post-transcriptional gene 
regulation. Furthermore, the Chakrabarti lab is embedded within a larger 
network of groups interested in both RNA biology as well as structural biology 
and offers a dynamic and international research environment. 

More information about the Chakrabarti group can be found at: 
https://www.bcp.fu-berlin.de/en/chemie/biochemie/research-groups/chakrabarti-group/index.html
 


The ideal candidate will hold a Masters degree in Biochemistry (or a very 
closely related discipline) and have a strong interest in protein-RNA 
biochemistry and structural biology. Good communication skills (in English), 
strong motivation and the ability to work in a team are essential. Prior 
experience in molecular biology and protein/RNA biochemistry will be valued.

Interested candidates are invited to apply with their CV, transcripts of 
Bachelors and Masters studies, a brief description of their Masters thesis 
project and the contact information of two referees. Applications should be 
submitted by email to chakr...@zedat.fu-berlin.de 
 and should mention “PhD position for mRNA 
decay” in the subject line. 

Please don’t hesitate to get in touch with me for informal enquiries and feel 
free to circulate this email among candidates who you think might be 
interested. 

With best wishes,
Sutapa

--
Sutapa Chakrabarti, Ph.D.
Institute of Chemistry and Biochemistry
Freie Universität Berlin
Takustr. 6 
14195 Berlin
Germany
Phone: +49-(0)30-83875094









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[ccp4bb] Assistant Professor Position at UC Davis

[James Anthony Letts]

Dear Colleagues,

I wanted to bring this great opportunity to join us at UC Davis as an Assistant 
Professor to the communities attention (https://recruit.ucdavis.edu/JPF03095):

The Department of Molecular and Cellular Biology, in the College of Biological 
Sciences, University of California, Davis, invites applications for a 
tenure-track faculty position at the ASSISTANT PROFESSOR level. The Department 
seeks outstanding candidates investigating fundamental questions in modern 
biology that will add to or complement existing strengths in structural biology 
and biochemistry.

Competitive applicants must have a Ph.D. (or equivalent) in biological 
sciences-related fields and have demonstrated outstanding potential in their 
field. Candidates will be expected to develop a strong dynamic independent 
research program and to share our commitment to scholarly undergraduate and 
graduate education. We are especially interested in candidates who demonstrate 
an ability to integrate multi-disciplinary approaches into their proposed 
research, including cryo-electron microscopy.
The BIOEM facility at UC Davis contains a new Thermo Scientific 200 kV Glacios 
electron microscope with GATAN K3 detector and autoloader. As well as a JEOL 
JEM-1230 electron microscope used for sample optimization via negative stain 
and a JEOL JEM-2100F electron microscope with Direct Electron (DE)-20 detector 
for cryoEM grid screening and optimization. The facility also contains an EMS 
100X glow discharger, FEI Vitrobot Mach III and Bench Top Turbo III carbon 
coater for cryoEM grid preparation. The facility manager Dr. Fei Guo has 
extensive experience with grid optimization and high-resolution data collection 
for single-particle cryoEM structure determination. In addition to the 
necessary computational resources for operating the microscopes the facility 
contains, two dual-GPU, 12-cpu computers and two Quad-GPU 24-cpu computers for 
on-the-fly and routine data processing, as well as a 130 TB storage array. 
Additionally, Computer Science and Engineering at UC Davis manages a 
high-performance computing cluster (named crick) for the Department of 
Molecular and Cellular Biology. As a member of the Molecular and Cellular 
Biology department your lab would have full access to these computational 
resources. Crick is composed of 29 nodes:  one head node, 12 nodes with 24 CPUs 
and 64 GB RAM each, four nodes with 32 CPUs and 64 GB of RAM each, two ‘bigmem’ 
nodes with 64 CPUs and 512 GB of RAM each and three GPU nodes operated by the 
Al-Bassam lab with 40 CPUs, 8 GPUs and 288 GB of RAM each.

We are a 90-minute drive from the Bay Area (depending on traffic ), which is 
home to many world-class research institutions and cryoEM resources. As members 
of the Bay Area Cryo-EM (BACEM) consortium we have regular monthly access to 
Titan Krios microscopes at UCSF and regular bi-annual meetings with other 
cryo-EM groups from Stanford, UC SF, UC Berkeley and industry. UC Davis also 
has easy access to two national cryo-EM centers: The National Center for 
Macromolecular Imaging (NCMI) at the SLAC National Accelerator Laboratory and 
the Pacific Northwest Center for Cryo-EM (PNCC) at Oregon Health Sciences 
University. These NIH-supported centers provide access to state of the art 
cryo-EM sample preparation equipment and microscopes.

I joined the department less than one year ago (November 2018) to set up my 
research program in Structural Biology and Biochemistry and it has been a 
really great experience. Everyone here is extremely supportive and are eager to 
invest in biochemistry and cryo-EM. We have fantastic undergrads, graduate 
students, facilities people and academic support. Although I am originally from 
North American (Canada), I came to Davis via Europe (IST Austria) and got great 
support throughout the whole process: relocation, visa application, permanent 
residency, home buying etc. So don’t hesitate to apply from anywhere in the 
world!

Overall it is a great place to live and set up your independent research 
program. Please don’t hesitate to contact me with any questions!

All the best,

James


James A Letts, PhD
Assistant Professor

jale...@ucdavis.edu
530-752-3193
Briggs Hall, Rm 25

Laboratory of Electron Transport Membrane Proteins and Structural Bioenergetics
Department of Molecular and Cellular Biology
University of California, Davis
Davis, CA 95616
USA
--




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Re: [ccp4bb] Propeptide cleavage for complex assembly

[Darren Hart]

Influenza polymerase heterotrimer expressed in insect cells (MultiBac 
technology) as a fully synthetic polyprotein with subunits separated by 
TEV sites



TevProtease-Tev-PA-Tev-PB1-Tev-PB2-Tev-CFP


Reich et al. Nature 2014; doi:10.1038/nature14009


/Extended Data Figure 1 | Production and characterization of influenza B//
//polymerase heterotrimer. a, Schematic of the self-cleaving polyprotein//
//construct used to express recombinant influenza B heterotrimeric 
polymerase//
//in insect cells. N-terminally it encodes the tobacco etch virus (TEV) 
protease//
//that cleaves C-terminal to the amino-acid sequence ENLYFQ (in italics) 
and//

//releases N-terminally His-tagged PA, PB1, C-terminally Strep-tagged PB2//
//and cyan fluorescent protein (CFP) for facilitated expression 
monitoring.//
//Arrows indicate the N-to-C-terminal direction and the termini of each 
mature//

//protein. The histidine and streptavidin tags are underlined./


Darren




On 02/10/2019 10:18, Paula Salgado wrote:

Dear colleagues

We have been working on a protein that is produced as a pro-peptide, 
cleaved internally and reassembled into a complex. The interacting 
regions are the new C and N-termini at the cleavage site, so no 
rearrangement or loss of part of the protein is involved. The 
resulting interacting region is quite intricate, with a helix bundle 
and beta-sheet composed of members of each partner protein.


I wonder if there are other examples of such processing required for 
folding/assembly of a functional complex? I'm not talking of 
processing involving removal of termini or internal regions like 
signal removal in transported proteins or maturation of preproinsulin, 
for example. I'm interested in examples where a propeptide is cleaved, 
then the two proteins reassemble in a complex via interactions of the 
similarly oriented new termini.


Any suggestions most appreciated.

Thanks a lot!
Paula



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--

**

Dr. Darren J. Hart,

CNRS Research Director, Institut de Biologie Structurale (IBS)
Unité Mixte de Recherche UMR5075 (CEA-CNRS-UGA)

Director, Integrated Structural Biology Grenoble (ISBG)
Unité Mixte de Service UMS3518 (CNRS-UGA-CEA-EMBL)

**

Email: darren.h...@ibs.fr

Tel: +33 4 57 42 85 86

Physical address: IBS/ISBG, 71 avenue des Martyrs, 38000 Grenoble, France

Postal address: IBS/ISBG, 71 avenue des Martyrs, CS 20192, 38042 
Grenoble, Cedex 9, France


**




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[ccp4bb] Propeptide cleavage for complex assembly

[Paula Salgado]

Dear colleagues

We have been working on a protein that is produced as a pro-peptide, cleaved 
internally and reassembled into a complex. The interacting regions are the new 
C and N-termini at the cleavage site, so no rearrangement or loss of part of 
the protein is involved. The resulting interacting region is quite intricate, 
with a helix bundle and beta-sheet composed of members of each partner protein.

I wonder if there are other examples of such processing required for 
folding/assembly of a functional complex? I'm not talking of processing 
involving removal of termini or internal regions like signal removal in 
transported proteins or maturation of preproinsulin, for example. I'm 
interested in examples where a propeptide is cleaved, then the two proteins 
reassemble in a complex via interactions of the similarly oriented new termini.

Any suggestions most appreciated.

Thanks a lot!
Paula



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[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] no tNCS and Phaser manuals

[Herman . Schreuder]

Dear Iracema,

Thank you very much for your hint of using CCP4i, I never use it but this time 
I should have used it to find out how to switch off the tNCS. Unfortunately, I 
cannot reach any of the phaser.cimr sites. I get the error message that our 
proxy server does not react. I can reach the phaser wiki at slac, but that one 
seems to be most recently updated in 2016 and most of the links produce “page 
not found” error messages.

I probably should contact our IT department what is wrong with our proxy 
server, since when our firewall blocks a site, it will tell so, which is not 
the case here.

Best,
Herman


Von: IRACEMA CABALLERO MUÑOZ 
Gesendet: Dienstag, 1. Oktober 2019 15:06
An: Schreuder, Herman /DE 
Cc: CCP4BB@jiscmail.ac.uk
Betreff: [EXTERNAL] Re: [ccp4bb] no tNCS and Phaser manuals


EXTERNAL : Real sender is icm...@ibmb.csic.es

Hi Herman, I made an image that shows how to turn off tNCS in CCP4i, CCP4i2 and 
Phenix.
[phaser_tncs.jpg]

In addition in the phaser wiki there are several tutorials and some other 
useful information:
https://www.phaser.cimr.cam.ac.uk/index.php/Tutorials


Best wishes,
Iracema Caballero

El mar., 1 oct. 2019 a las 14:45, 
mailto:herman.schreu...@sanofi.com>> escribió:
Dear community,

I wanted to switch off the tNCS for a Phaser run, but could not find any Phaser 
manuals online, explaining how to do this.
So I have two questions:

  1.  How do I switch off tNCS in Phaser and
  2.  Are there any phaser manuals online? I tried hard to find them using 
Bing, but the websites were either not present, not available or could not be 
found. It may be that our firewall is also blocking certain sites although most 
sites are accessible.

Thank you very much for your help!
Herman






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