[ccp4bb] offtopic: three job postings @ Silicon Therapeutics

[Artem Evdokimov]

Dear CCP4 friends,

I would like to let you know that we have just posted three jobs open
within my team at Silicon Therapeutics. Qualified inquiries are welcome!

Artem

1. Senior position in Biochemistry

https://silicontx.com/careers/open-positions/senior-investigator-principal-investigator-biochemistry/

2. Mid-to-senior position in Biophysics/Structure

https://silicontx.com/careers/open-positions/investigator-senior-investigator-principal-investigator-biophysics-structural-biology/

3. Research associate in Biochemistry/Biophysics/Structure

https://silicontx.com/careers/open-positions/research-associate-biochemistry-biophysics-structural-biology/



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Re: [ccp4bb] A postdoctoral fellow position at Dana-Farber Cancer Institute and Harvard Medical School, Boston, USA

[Tan, Kemin]

Dear all,

A postdoctoral fellow position is currently available at Dana-Farber Cancer 
Institute and Harvard Medical School, Boston, USA

The collaborative Prof. Jia-huai Wang and Prof. Ellis Reinherz labs at 
Dana-Farber Cancer Institute and Harvard Medical School are recruiting a 
postdoctoral fellow to study structural immunology. We use interdisciplinary 
approaches at the interface of structural, molecular mechanism of cellular 
immunity with the aim of translating these insights into immunotherapy. 
Specific research directions include structural and molecular studies of T cell 
development. The laboratory provides a full access to cutting-edge techniques 
in molecular biology, protein chemistry, NMR and protein crystallography.

Highly-motivated candidates with a recent PhD or MD/PhD in structural biology 
and significant experience in molecular biology, biochemistry and immunology 
are encouraged to apply. Skills in molecular cloning, protein chemistry and 
crystallography are essential. Candidates should have a publication record in 
peer-reviewed journals. We are seeking a candidate with excellent writing and 
communication skills, able to work independently but also effectively with 
other lab members. Applicants should include a short statement of research 
goals, CV and three references with their application.

Please contact Prof. Jia-huai Wang at 
jw...@crystal.harvard.edu.




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[ccp4bb] slightly offtopic: antibody and nanobody development providers

[Artem Evdokimov]

Dear CPP4ers

Once again I would like to refill my cup of borrowed wisdom from the
collective fountain that is this excellent list :)

I am looking to make antibodies/nanobodies for crystal-chaperone
(nano/Fab/ScFv etc) kind of a deal. I have a few providers from my past
endeavors, but really would like to gather some new ones especially if
people used them and liked the net result. Would be happy to summarize the
outcome and distribute the summary in this list.

Many thanks,

Artem

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[ccp4bb] Faculty position at Case Western Reserve University: Tenure Track Assistant or Associate Professor of Biochemistry

[Focco Van den Akker]

Dear all,

Case Western Reserve University, Department of Biochemistry invites
applications for tenure-track faculty or tenured faculty positions. While
applications from individuals with interests in any area of biochemistry
are requested, areas of specific interest include metabolism/metabolomics,
RNA biology, stress response signaling, and chromatin biology as they
pertain to fundamental aspects of human diseases such as cancer biology.

More details are here in the ad posted on the ASBMB website:
https://careers.asbmb.org/job/assistant-or-associate-professor/54848389/

Thank you,
Focco

-- 
Focco van den Akker, Ph.D.
Associate Professor
Search Committee Chair for Tenure-Track Faculty
Department of Biochemistry RT500
School of Medicine
Case Western Reserve University
10900 Euclid Avenue
Cleveland, OH 44106-4935
phone:  (216) 368-8511
fax:(216) 368-8845
E-mail: focco.vandenak...@case.edu
Faculty webpage:
http://www.cwru.edu/med/biochemistry/faculty/vandenakker.html
Lab webpage:
http://www.cwru.edu/med/biochemistry/vandenAkker_lab/index.html



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[ccp4bb] Newcastle University Professor/Reader/Senior Lecturer of Structural Biology

[Arnaud Basle]

Dear All,

Newcastle University is delighted tobe recruiting for a Professor / 
Reader / Senior Lecturer of Structural Biology to work within the 
Biosciences Institute in the Faculty of Medical Sciences.


https://jobs.ncl.ac.uk/job/Newcastle-ProfessorReaderSenior-Lecturer-of-Structural-Biology/623899301/

Cheers,

Arnaud

--
Dr Arnaud Basle X-ray facilities manager
Newcastle Structural Biology Laboratory
Biosciences Institute
Faculty of Medical Sciences
Newcastle University
Framlington place
NE2 4HH Newcastle upon tyne
Phone 0191 208 5482




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[ccp4bb] S2C2 CryoEM CCP-EM Modeling Workshop, November 10-13, 2020

[Dunn, Lisa B.]

S2C2 Workshop - CryoEM CCP-EM Modeling
Stanford-SLAC Cryo-EM Center (S2C2) will offer a modeling workshop held via 
Zoom Webinar between November 10-13, 2020 from 8:00 AM - 2:00 PM (PDT) daily.  
This workshop will give participants an introduction to atomic model building 
into cryo-EM maps using the tools available in the CCP-EM software suite.  
There is no cost for this workshop.  Please visit the workshop 
website
 to apply by 5:00 PM (PDT) on November 2, 2020.
Our guest trainers for this event are:

-  Dr. Colin Palmer, CCP-EM, STFC Rutherford Appleton Laboratory

-  Dr. Tom Burnley, CCP-EM, STFC Rutherford Appleton Laboratory

-  Dr. Kevin Cowtan, Dept. of Chemistry, University of York

-  Prof. Paul Emsley, MRC-LMB, Cambridge

-  Asst. Prof. Arjen Jakobi, Dept. of Bionanoscience, TU Delft

-  Dr. Agnel Praveen Joseph, CCP-EM

-  Dr. Robert Nicholls, MRC-LMB, Cambridge

-  Prof. Maya Topf, CCP-EM, ISMB Birkbeck, University of London

-  Dr. Martin Winn, CCP-EM.
Organizers:  Prof. Wah Chiu, Dr. Michael Schmid, Stanford University, and Dr. 
Colin Palmer, CCP-EM, STFC Rutherford Appleton Laboratory

The 
S2C2
 is supported by the National Institutes of Health Common Fund Transformative 
High Resolution Cryo-Electron Microscopy 
program.





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[ccp4bb] postdoctoral position in the Houry lab at the University of Toronto

[Walid Houry]

A postdoctoral position is available immediately in the Dr. Walid A. Houry's 
group for an excellent trainee to study the structure and function of molecular 
chaperones and ATP-dependent proteases. The successful candidate will have a 
PhD in Chemistry, Biochemistry, Molecular Biology or a related field. Strong 
knowledge of X-ray crystallography and cryoEM is required for this position. 
For more information about the projects, refer to the lab website:
http://lab.walidhoury.com/


Please forward a cover letter and CV to
walid.ho...@utoronto.ca


Address is below.

---
Dr. Walid A. Houry, PhD
Professor
Department of Biochemistry, Faculty of Medicine
Department of Chemistry, Faculty of Arts and Science
University of Toronto
661 University Avenue
MaRS Centre, West Tower, Room 1612
Toronto, ON M5G 1M1
CANADA

Phone (416) 946-7141 office, (416) 946-7364 lab
FAX (416) 978-8548
Email walid.ho...@utoronto.ca
Web http://lab.walidhoury.com
---




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[ccp4bb] Scientist-I (Structural Biology) position at Frederick National Laboratory for Cancer Research

[Dhirendra K Simanshu]

Hello everyone,

The Frederick National Laboratory for Cancer Research is looking for a
Scientist-I with experience in protein chemistry and structural biology.
The candidate will join the structural biology group within the NCI RAS
Initiative program and work on the protein-small molecule complexes.

For detailed information and to apply for this position, please use this
link:
https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4=leidosbiomed=1404


Best regards
Dhirendra Simanshu



--

Dhirendra Simanshu

Principal Scientist, Team Lead - RAS Structural Biology

NCI RAS Initiative

Frederick National Laboratory for Cancer Research

Leidos Biomedical Research, Inc.

*Office/Courier*: 8560 Progress Drive, C1012, Frederick, MD 21701

*USPS mail*: Post Office Box B, ATRF-C1012, Frederick, MD 21702

dhirendra.siman...@fnlcr.nih.gov 



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Re: [ccp4bb] challenging data for indexing

[Xu, Shenyuan]

Dear everyone,

I also want to thank Andrew for imosflm to give me the right direction. I
have also successfully indexed the data with imosflm.

Thanks!

Best wishes,

Shen

On Mon, Oct 5, 2020 at 8:50 AM Xu, Shenyuan  wrote:

> Dear everyone,
>
> Thanks for all the suggestions! I am sorry if I did not respond to your
> emails and say thanks individually.
>
> For the dataset 1, the data has been successfully indexed with Dials and
> XDS after readjusting beam center and rotation axis handedness. Thanks
> David for providing me the Dials commands and Kay for giving me the XDS
> codes.
>
> I really appreciate the help from all of you!
>
> Thanks,
>
> Shen
>
> On Fri, Oct 2, 2020 at 11:04 AM Xu, Shenyuan  wrote:
>
>> Dear CCP4 community,
>>
>> I have two challenging datasets for indexing, one has very strong
>> diffraction, the other one has very weak spots. I know both crystals are
>> not very good, knocked down from a big chunk of crystal.
>>
>> For the dataset 1, first I use iMosflm to index it, but it can not refine
>> it as "Detector tilt and twist parameters vary substantially". Based on the
>> penalty value and RMSD, the index solution is not satisfactory. Then I
>> moved to Xia2 from CCP4i, no index solution was found. Then I use Dials, it
>> can successfully index the data, but only about 25% spots have been
>> indexed, and the rmsd is not very good. I forced it to proceed, and after
>> integration, the statistics seem to be good, but I can not use MR to solve
>> the structure (If the index is good, I think MR can solve it as I did it
>> before). I have gone through all the troubleshooting suggestions that are
>> available online for iMosflm and Dials, but no improvement.
>>
>> For the dataset 2, I think the main reason is because of the weak
>> diffraction. Both iMosflm and Dials can not give good results.
>>
>> The best way may be to optimize the crystal. But I feel like there may be
>> a better way to optimize the parameters to index it. The datasets are
>> large, I can send you privately by email if you are interested to take a
>> look.
>>
>> I really appreciate your suggestions.
>>
>> Thanks,
>> Shen
>>
>>
>



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Re: [ccp4bb] challenging data for indexing

[Xu, Shenyuan]

Dear everyone,

Thanks for all the suggestions! I am sorry if I did not respond to your
emails and say thanks individually.

For the dataset 1, the data has been successfully indexed with Dials and
XDS after readjusting beam center and rotation axis handedness. Thanks
David for providing me the Dials commands and Kay for giving me the XDS
codes.

I really appreciate the help from all of you!

Thanks,

Shen

On Fri, Oct 2, 2020 at 11:04 AM Xu, Shenyuan  wrote:

> Dear CCP4 community,
>
> I have two challenging datasets for indexing, one has very strong
> diffraction, the other one has very weak spots. I know both crystals are
> not very good, knocked down from a big chunk of crystal.
>
> For the dataset 1, first I use iMosflm to index it, but it can not refine
> it as "Detector tilt and twist parameters vary substantially". Based on the
> penalty value and RMSD, the index solution is not satisfactory. Then I
> moved to Xia2 from CCP4i, no index solution was found. Then I use Dials, it
> can successfully index the data, but only about 25% spots have been
> indexed, and the rmsd is not very good. I forced it to proceed, and after
> integration, the statistics seem to be good, but I can not use MR to solve
> the structure (If the index is good, I think MR can solve it as I did it
> before). I have gone through all the troubleshooting suggestions that are
> available online for iMosflm and Dials, but no improvement.
>
> For the dataset 2, I think the main reason is because of the weak
> diffraction. Both iMosflm and Dials can not give good results.
>
> The best way may be to optimize the crystal. But I feel like there may be
> a better way to optimize the parameters to index it. The datasets are
> large, I can send you privately by email if you are interested to take a
> look.
>
> I really appreciate your suggestions.
>
> Thanks,
> Shen
>
>



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