Re: [ccp4bb] MR solution not working

[Bruno KLAHOLZ]

Hello,

are the low resolution data complete?
How do the statistics look like (completeness, I/sigma etc.)?
Missing low resolution data (e.g. hidden by the beam stop) can create problems 
in MR.
Any axis aligned along the rotation axis by bad luck (would benefit from offset 
during data collection)?
Ice rings or other problems leading to rejections in a systematic region?

Best,

Bruno


From: CCP4 bulletin board  On Behalf Of Shubhashish 
Chakraborty
Sent: 03 March 2022 05:44
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] MR solution not working

Hello,
I am trying to solve a dataset using molecular replacement. However, neither 
Phaser MR nor Molrep can give any solution.
In Phaser, I have received an advisory that Top FTF has not packed.
I have tried molecular replacement using the wild-type protein at different 
resolutions (I am working on a mutant).
Also, I have truncated the loops from the input structure. However, none have 
worked.
So, what can be the possible way to solve this data set?

Thank you

Shubhashish Chakraborty
PhD JRF 2018
Structural and Molecular Biology Lab (Varma Lab)
Advanced Centre for Treatment, Research and Education in Cancer (ACTREC)
Khargar, Navi Mumbai
E-mail: schakrabo...@actrec.gov.in



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Re: [ccp4bb] MR solution not working

[Eleanor Dodson]

Well - there are various traps towards a MR solution.
Maybe the data is not very good? What is the resolution and merging r
factor?

Assuming data is ok...
Most common is that the spacegroup is wrong. Have you tested all possible
spacegroups for the Laura group? Both phaser and molrep have options to do
this.

If there are many copies in the asymmetric unit that could make it
difficult..

You say it is a mutant - is the spacegroup and cell similar to the native
protein? If that is so you could probably take the native molecule as the
“solution” and start refinement from it.

But sometimes a dataset has got mislabelled and is actually from a
different source altogether. The simbad procedure can look for matches and
sometimes finds an answer.

Give me some more details of your project and perhaps I can help more.
Eleanor


On Thu, 3 Mar 2022 at 05:20, Shubhashish Chakraborty <
750c9a1ca48b-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello,
> I am trying to solve a dataset using molecular replacement. However,
> neither Phaser MR nor Molrep can give any solution.
> In Phaser, I have received an advisory that Top FTF has not packed.
> I have tried molecular replacement using the wild-type protein at
> different resolutions (I am working on a mutant).
> Also, I have truncated the loops from the input structure. However, none
> have worked.
> So, what can be the possible way to solve this data set?
>
> Thank you
>
> Shubhashish Chakraborty
> PhD JRF 2018
> Structural and Molecular Biology Lab (Varma Lab)
> Advanced Centre for Treatment, Research and Education in Cancer (ACTREC)
> Khargar, Navi Mumbai
> E-mail: schakrabo...@actrec.gov.in
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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[ccp4bb] Sv: [ccp4bb] MR solution not working

[Casper Wilkens]

Are the mutant and wild-type in the same space group and are the unit cell 
dimensions similar? If so, a simple rigid body refinement could work.

Fra: CCP4 bulletin board  på vegne af Shubhashish 
Chakraborty <750c9a1ca48b-dmarc-requ...@jiscmail.ac.uk>
Sendt: 3. marts 2022 05:43:42
Til: CCP4BB@JISCMAIL.AC.UK
Emne: [ccp4bb] MR solution not working

Hello,
I am trying to solve a dataset using molecular replacement. However, neither 
Phaser MR nor Molrep can give any solution.
In Phaser, I have received an advisory that Top FTF has not packed.
I have tried molecular replacement using the wild-type protein at different 
resolutions (I am working on a mutant).
Also, I have truncated the loops from the input structure. However, none have 
worked.
So, what can be the possible way to solve this data set?

Thank you

Shubhashish Chakraborty
PhD JRF 2018
Structural and Molecular Biology Lab (Varma Lab)
Advanced Centre for Treatment, Research and Education in Cancer (ACTREC)
Khargar, Navi Mumbai
E-mail: schakrabo...@actrec.gov.in



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Re: [ccp4bb] MR solution not working

[Ethan A Merritt]

On Wednesday, 2 March 2022 20:43:42 PST Shubhashish Chakraborty wrote:
> Hello,
> I am trying to solve a dataset using molecular replacement. However, neither 
> Phaser MR nor Molrep can give any solution. 
> In Phaser, I have received an advisory that Top FTF has not packed. 
> I have tried molecular replacement using the wild-type protein at different 
> resolutions (I am working on a mutant).
> Also, I have truncated the loops from the input structure. However, none have 
> worked. 
> So, what can be the possible way to solve this data set?

Double check your space group.
Then check it again.
If there is any chance you integrated the data in the wrong space
group, go back and process it again with lower symmetry.

Break the model into domains; feed phaser the individual domains for
separate placement.

good luck

Ethan


>  
> Thank you
>  
> Shubhashish Chakraborty
> PhD JRF 2018
> Structural and Molecular Biology Lab (Varma Lab)
> Advanced Centre for Treatment, Research and Education in Cancer (ACTREC)
> Khargar, Navi Mumbai
> E-mail: schakrabo...@actrec.gov.in
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



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[ccp4bb] MR solution not working

[Shubhashish Chakraborty]

Hello,

I am trying to solve a dataset using molecular replacement. However, neither Phaser MR nor Molrep can give any solution. 

In Phaser, I have received an advisory that Top FTF has not packed. 

I have tried molecular replacement using the wild-type protein at different resolutions (I am working on a mutant).

Also, I have truncated the loops from the input structure. However, none have worked. 

So, what can be the possible way to solve this data set?

 

Thank you

 




Shubhashish Chakraborty

PhD JRF 2018

Structural and Molecular Biology Lab (Varma Lab)

Advanced Centre for Treatment, Research and Education in Cancer (ACTREC)

Khargar, Navi Mumbai


E-mail: schakrabo...@actrec.gov.in








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[ccp4bb] Research Fellow Position - Structural Biology of Host-Pathogen Interactions (Toronto, Canada)

[Jean-Philippe Julien]

Job description
Dr. Julien’s laboratory at The Hospital for Sick Children Research Institute is 
looking for a Research Fellow to join our Structural Biology team. The 
successful candidate will participate in the characterization of host-pathogen 
interactions by using a combination of in silico, biochemical, biophysical, 
structural, and protein engineering techniques. We are looking for a driven and 
enthusiastic scientist who demonstrates passion and creativity towards the 
structure-function study of important pathogenic targets and who can thrive in 
a highly-collaborative setting.

Roles & Responsibilities

  *   Optimize library designs from in silico structural principles leveraging 
latest developments in structure prediction algorithms;
  *   Design and optimize constructs for expression in E.coli and mammalian 
cells;
  *   Biophysically characterize purified constructs for their Tm, Tagg and 
polydipersity, and perform ITC and BLI binding experiments to determine binding 
thermodynamics and kinetics;
  *   Use Cryo-Electron Microscopy to determine the structure of designed 
constructs in complex with their receptors to enable iterative structure-based 
design.
Desired Skills and Experience

  *   Structural Biologist with a PhD in Biochemistry, Molecular Biology, 
Computational Biology or related field;
  *   Strong knowledge in using Cryo-Electron Microscopy to study protein 
structure, especially in a context of structure-guided design;
  *   Experience in protein engineering, molecular biology, protein expression 
in various systems, purification and biophysical characterization;
  *   Practical experience in using in silico approaches to improve binding 
interfaces is a plus;
  *   Demonstrated ability to participate in collaborative scientific projects;
  *   Organization skills, efficiency and meticulous record keeping.
How to Apply?
Send your CV and a letter of intent to 
jean-philippe.jul...@sickkids.ca 
before March 31st, 2022. Successful candidates will be notified for interviews, 
at which time two letters of reference will also be required.

About Us
Dr. Julien's laboratory (https://lab.research.sickkids.ca/julien/) focuses on 
the molecular characterization of biologics by studies of their interactions 
with cell surface receptors in therapeutic development, and with pathogens 
guiding vaccine design primarily against Plasmodium falciparum malaria, HIV-1, 
and COVID-19. Dr. Julien’s laboratory is located in the Molecular Medicine 
Program of The Peter Gilgan Centre for Research and Learning at SickKids, a 
21-story, 750,000 square-foot facility in downtown Toronto that incorporates an 
open-concept design, state-of-the-art research facilities, and collaborative 
work spaces.
As a member of the SickKids community, you will become part of a world-renowned 
organization dedicated to fulfilling a vision of Healthier Children, A Better 
World. For over 135 years, SickKids has worked hard to make the world a better 
place for children and their families. Each day, people around the organization 
are doing meaningful work that directly, and often indirectly, benefits 
children in Canada and around the world.




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[ccp4bb] Open Positions at Rigaku

[Joseph Ferrara]

Posted on behalf of Mark Benson:

Rigaku has two open positions in the US for Single Crystal Regional Account 
Managers. Ideally, one position will be East Coast-based and the other and West 
Coast-based. However, all US locations will be considered.

Either opportunity would be an excellent choice to launch a career after 
completing a Ph.D. or postdoc at an extremely exciting time with the launch of 
our Electron Diffractometer, the Synergy-ED.

Please pass on to any potentially interested candidates in your groups or to 
collaborators in the US.

For informal discussions, please contact Mark: 
mark.ben...@rigaku.com

East
https://www.rigaku.com/job/rigaku-americas-corporation/east-coast-regional-account-manager-us

West
https://www.rigaku.com/job/rigaku-oxford-diffraction-rigaku-americas-corporation/west-coast-regional-account-manager-us



Joseph D. Ferrara, Ph.D., NREMT
CSO, Rigaku Americas Corporation
Deputy Director, X-ray Research Laboratory, Rigaku Corporation
Vice-Chair, US National Committee for Crystallography
Treasurer, Council of Scientific Society Presidents

[cid:image001.png@01D82E4B.180BEFD0]

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[ccp4bb] Reminder: INSTRUCT-ESRF workshop on sample preparation for cryo-EM, May 23-25, 2022

[David FLOT]

Dear all,

This is a kind reminder to apply to our INSTRUCT-ESRF workshop on the 
cryo-EM sample preparation.  The deadline is approaching soon. For 
details, please see the message below.


Best
Isai


We are pleased to announce our 2.5-day practical workshop on sample 
preparation for single particle cryo-EM from *May**23^rd to 25^th2022*. 
This is the fourth of a series of practical hands-on workshops and is 
aimed at PhDs, PostDocs and scientists new to the field of single 
particle cryo-EM. During the course, participants will learn theoretical 
and practical aspects of sample preparation for single particle cryo-EM 
including prior quality control by negative staining.


There is*no registration fee*and meals and accommodation during the 
workshop will be provided free of charge. However, participants are 
expected to arrange and pay for their own travel to/from Grenoble. A 
maximum of 12 participants will be selected and we will accept a limited 
number of participants’ samples to be tested during the workshop.


Application for the workshop isopen 
and the*deadline for application 
is March 20^th , 2022*. Successful candidates will be informed during 
the first week after the deadline. For more information, please 
consulthttps://www.esrf.fr/cryo-em1-2022


This is currently planned as an in-person workshop and is co-funded by 
INSTRUCT (IBS).


Best regards,
Isai (on behalf of the organizing committee)

--

 
Dr David FLOT

Beam-Line Operation Manager Tel : (+33) 4 76 88 17 63
Structural Biology GroupFax : (+33) 4 76 88 26 24
ESRF
e-mail :david.f...@esrf.fr  http://www.esrf.eu
Room: 30.1.13

Physical addressPostal address
ESRF-The European Synchrotron   ESRF-The European Synchrotron
71, Avenue des Martyrs  CS40220
Grenoble, France38043 Grenoble Cedex 9
France



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[ccp4bb] Why there are two solutions about heavy atoms in SHELXD

[fu]

Dear Colleagues,
   I get two solutions after running SHELX C/D. In both results, the 
coordinates of the heavy atoms are centrosymmetric. Why there are two solutions?

Best wishes,
Fu Xingke
Institute of Physics CAS


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[ccp4bb] RESEARCH METHODOLOGY CONFERENCE (DEADLINE EXTENDED TO 13 MARCH 2022

[The London Institute]

Dear All,

I am writing in regard to the "RESEARCH METHODOLOGY CONFERENCE (RMC-2022): 
Conducting Research and Revisiting Research Methods in Education and Doctoral 
Studies in the (Post) COVID-19 Era: Challenges and Opportunities" organised in 
partnership with Coventry University. Please see the details below. 

RESEARCH METHODOLOGY CONFERENCE (RMC-2022)

Conducting Research and Revisiting Research Methods in Education and Doctoral 
Studies in the (Post) COVID-19 Era: Challenges and Opportunities 
 
ABSTRACT SUBMISSION DEADLINE: 13 MARCH 2022 (EXTENDED)


For More 
information:https://thelondoninstitute.org.uk/research-methodology-conference-rmc-2022/
 


The London Institute invites you to submit an abstract to the Research 
Methodology Conference (RMC-2022) that will be held in partnership with 
Coventry University’s Centre for Global Learning (GLEA) on 20th April, 2022.

The conference invites abstracts including but not limited to the following 
topics: 

Methodological choices and challenges; 

Research design, methods of data collection and fieldwork and analysis; 

Decolonising research methodologies; 

Ethical and legal issues; 

Digital Research, use of new technological tools and innovative approaches; 

Presentation and dissemination of research outcomes; 

Engaging marginalised audiences in research; 

Limitations and future directions; 

EXPERTS SESSION: RE-CONCEPTUALISING RESEARCH IN THE POST COVID ERA 

Prof. Lynn Clouder, Director, Institute for Global Education, Coventry 
University, UK 

Prof. Megan Crawford, Theme Lead Education Leadership and Policy, Coventry 
University, UK 

Prof. Suzanne Clisby, Theme Lead Gender, Equality and Diversity, Coventry 
University, UK

Prof. Julia Carroll, Theme Lead Development, Engagement and Attainment, 
Coventry University, UK 

Prof. Katherine Wimpenny, Theme Lead Global Learning: Education without 
Boundaries, Coventry University, UK 

KEYNOTES SESSION ​1: DIGITALISING RESEARCH 

Dr Jeremy Knox, Co-director of the Centre for Research in Digital Education 
(Data Society) and a Lecturer in Digital Education, The University of 
Edinburgh, UK 

•   Title: “(Post) Digital Methods for (Post) Pandemic Times”

Dr Adam Crymble, Lecturer of Digital Humanities, Department of Information 
Studies, University College London, UK 
 
•   Title: “Building Methods with the Global South” 

KEYNOTE SESSION ​2: 

Prof. Lynette Jacobs, Comparative and International Education, University of 
the Free State, South Africa 

•   Title: “Authentically Journeying Research with Yourself and Others”
 

Submission: 

Abstract should be no more than 500 words, outlining your study and the 
methodological aspect(s).  

Please submit your abstract via: 
https://easychair.org/conferences/?conf=rmc2022 

Abstract submission deadline : 13 March 2022 (Extended)

Paper notification : 28 March 2022

Presenter/ Attendee registration deadline : 11 April 2022

Conference : 20 April 2022

Registration and fees: For more information, please click here.  

Presenter:  £50 

Participant: £20  
 

Outcome: Post-Conference Publications 

I) Conference Proceedings:
Presented abstracts from the conference to be invited for a full paper 
submission for the Conference Proceedings to be published around September or 
October 2022. 

II) Special Issue of Review of Social Studies (RoSS):
The Conference Proceedings will follow with a Special Issue of selected papers 
(successfully going through the peer-review process) to be published at Review 
of Social Studies (RoSS)  around February 2023. 

Copyright © 2021 THE LONDON INSTITUTE OF SOCIAL STUDIES, All rights reserved.

Our mailing address is:
The London Institute of Social Studies
Hamilton House, 4 Mabledon Place,
London, WC1H 9BB, United Kingdom



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[ccp4bb] Protein Expression and Purification Scientist

[Andres PALENCIA]

Dear colleagues 

The following position is available in Grenoble (France):
Protein Expression and Purification Scientist, Biochemist, Structural Biologist

Job Description
A research technician position is available in the group Structural Biology of 
Novel Drug Targets in Human Diseases (https://noveltargets-palencia.com 
), at the Institute for Advanced 
Biosciences (Grenoble) to work on the expression, purification of protein-RNA 
complexes for structural studies, and their interactions with inhibitors in the 
field of infectious diseases and cancer.
In addition to structural biology and biophysical techniques, our laboratory 
also uses a wide range of approaches, from biochemistry and genetics to in vivo 
animal studies (in collaboration). We seek an outstanding candidate with 
training in molecular biology, protein/RNA biochemistry, with a strong interest 
in structural biology –crystallography or cryo-electron microscopy (EM)– to 
support the study of novel protein drug targets.

The successful candidate will use the in-house IAB facilities for protein 
production in different systems; other structural biology facilities of the 
Partnership for Structural Biology in Grenoble (EMBL-ESRF-IBS-ILL, 
http://www.psb-grenoble.eu ); and will interact 
with industrial partners.

Applicants should possess experience in molecular biology and protein 
production by using mammalian cells, bacteria or insect cells. Experience in 
the assembly and purification of protein-RNA complexes, crystallization and/or 
preparation of samples for EM studies would be an advantage. Motivation to work 
in a multidisciplinary and international environment is fundamental.

The candidate will work in the heart of the French Alpes (Grenoble) at the 
Institute for Advanced Biosciences (IAB), where creativity and excellence are 
fundamental to advance biomedical research and science education.  The IAB is a 
research center of the University of Grenoble-Alpes, the French National 
Institute of Health and Medical Research (INSERM), and the French National 
Center for Scientific Research (CNRS). Grenoble provides access to 
state-of-the-art structural biology technologies available at the ESRF, EMBL, 
IBS and ILL. This includes new EM facilities equipped with Titan Krios, and 
Glacios/Falcon III. Other facilities include the ESRF synchrotron X-ray 
beamlines, high-field NMR at the IBS as well as the high-throughput 
crystallization platform at the EMBL, mammalian and insect cell facilities, and 
the biophysical platform. The lab has access to other synchrotrons: DLS, DESY, 
SOLEIL, and SLS.

Applicants should provide a motivation letter and a CV with contact information 
for two or more referees.
For additional information please visit:

Research Group Website: https://noveltargets-palencia.com 
   

Job Location: Grenoble, France

Position Type: Full-Time/Regular

Starting Contract: 24 Months (renewable)

Starting Date: Immediate to summer 2022

Contact: andres.palen...@univ-grenoble-alpes.fr 
 
*
*
Dr. Andrés Palencia
National Institute of Health and Medical Research (Inserm)
Institute for Advanced Biosciences (IAB), Grenoble, Inserm–UGA–CNRS
Group Leader of Structural Biology of Novel Drug Targets in Human Diseases
Webpage: https://noveltargets-palencia.com
Phone: +33 (0) 476 54 95 75
ORCID:   orcid.org/-0002-1805-319X 

*
Address:
Institute for Advanced Biosciences (IAB), Inserm–UGA–CNRS
Site Santé, Allée des Alpes,
38700 La Tronche, France
Email: andres.palen...@univ-grenoble-alpes.fr
*
*




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Re: [ccp4bb] SHELXD for help

[Kay Diederichs]

On Tue, 1 Mar 2022 18:06:34 +0800, fu  wrote:

>Dear Colleagues,
>I have two question.
>The first question is, in SHELXD, they use XPREP to calculate the 
> correlation coefficient(CCano) between the signed anomalous differences at 
> different wavelengths? What’s the meaning? And how to calculate it?  The 
> reference is 《Schneider, T.R. & Sheldrick, G.M. (2002). "Substructure 
> Solution with SHELXD", Acta Crystallogr. D58, 1772-1779》
> ...

Hello Fu,

SHELXD uses data that may come from XPREP or SHELXC (or other programs). SHELXC 
is available as part of CCP4 (like SHELXD) and has part of the functionality of 
XPREP; XPREP however is not free. SHELXC (or other programs) calculate CCano. 
Please see 
https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php?title=XPREP and 
https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php?title=SHELX_C/D/E .

Hope this helps,
Kay



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