Re: [ccp4bb] Using EMAN2.

[Tom Calcraft]

Hi Gurudatt,

If the alignment of the tilt series is already good enough (this also applies 
to .ali stacks from IMOD), you can run eman2 tomogram reconstruction using the 
—noali and —niter=0 options, which will just reconstruct your tilt series in 
their current alignment. Note that the tilt axis should lie along the Y axis in 
the aligned stacks.

Also, this question would be better addressed to the EMAN2 Google group 
(https://groups.google.com/g/eman2), or alternatively the 3dem or ccpem mailing 
lists.

Best regards,
Tom


On 22 Mar 2022, at 13:53, Gurudatt Patra 
mailto:gurudatt1...@gmail.com>> wrote:


External Sender: Use caution.

Dear All,

I was wondering if we can use the aligned tilt series that we get from Serial 
EM as raw data directly for reconstruction and particle picking in EMAN2.
Thank you so much in advance.

Sincerely,
Gurudatt



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[ccp4bb] Rapid Access time at NE-CAT / APS

[Salbego, Cyndi]

Hello,

The end of the 2022-1 run at the APS is coming to a close on April 27th.  
Openings at the end of the run are rare, but we do have some availability for 
the last week of March and early to mid April.

To find out more about what NE-CAT has to offer please see the following:

https://necat.chem.cornell.edu/technical-specifications-24-id-c-beamline

https://necat.chem.cornell.edu/technical-specifications-24-id-e-beamline

Since this is a short time frame, being an already registered APS user would be 
easiest, but if you need to register please follow this information:  
https://necat.chem.cornell.edu/register

Any other questions, please contact us!

Cyndi Salbego
Administrator, NE-CAT







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[ccp4bb] Exciting opportunities at the CeTPD in Dundee

[Valentina Spiteri]

Dear CCP4 network, 

We have two very exciting Structural Biology/ Biophysics positions at the 
University of Dundee in the new Centre for Targeted Protein Degradation 
 within the Ciulli Group in 
collaboration with Boehringer Ingelheim using a range of techniques to guide 
the development of novel PROTACs. 

The CeTPD is a great place to work if you enjoy interdisciplinary and team 
science! 

Research Scientist (Post-doctoral level)
https://www.jobs.dundee.ac.uk/fe/tpl_uod01.asp?s=4A515F4E5A565B1A=105541,0286529865=149872024=62586121798676=sefptvkaqybotizzcw
 

 
Associate Scientist (post-graduate/masters level)
https://www.jobs.dundee.ac.uk/fe/tpl_uod01.asp?s=4A515F4E5A565B1A=105536,5686527923=149872024=62586121798676=setjfypdiqskpvjytc
 


Best wishes, 

Valentina Spiteri 


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[ccp4bb] Bioinformatician position at PDBe - closing Friday

[David Armstrong]

Dear Colleagues,

We are looking to recruit a structural bioinformatician who is 
interested in protein domains and functional annotations to join the 
Protein Data Bank in Europe (PDBe) team at the European Bioinformatics 
Institute (EMBL-EBI). This is a collaborative project between PDBe, the 
SCOP team at the MRC Laboratory of Molecular Biology (LMB).


This is a technical role, working together with developers and curators 
from PDBe and SCOP to improve a domain assignment tool, improve and 
further automate domain identification in multi-domain proteins, and 
help expand fold libraries. The successful candidate will also 
contribute to designing and implementing PDBe-KB web pages focused on 
aggregating structural data for specific structure domains.


The closing date for this post is 25th March 2022.

For more information on the position, please visit:
https://www.ebi.ac.uk/pdbe/about/jobs

Kind regards,
David Armstrong

--
David Armstrong
Outreach and Training Coordinator
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492544



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[ccp4bb] Using EMAN2.

[Gurudatt Patra]

Dear All,

I was wondering if we can use the aligned tilt series that we get from
Serial EM as raw data directly for reconstruction and particle picking in
EMAN2.
Thank you so much in advance.

Sincerely,
Gurudatt



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