Re: [ccp4bb] PDB deposition of structure solved with a Robetta model

[Jan Abendroth]

Hi Bernhard,
That sounds fine. I have used the term 'RoseTTAfold/AlphaFold2 model' in
that field for a few SSGCID depositions.
Many times, this field does not really provide an accurate description of
the model that was used: You might trim a model, use separate domains, use
MoRDa that might select domains from various sources, etc.

Cheers,
Jan


On Mon, Feb 7, 2022 at 5:24 AM Loll, Bernhard 
wrote:

> Dear all,
>
> I have recently solved a structure by molecular replacement with a
> search model calculated by the Robetta server.
>
> I am in the process to deposit the coordinates. Now, I am wondering
> which information I should give on the starting model. Routinely, I
> would provide the the PDB code, which is a mandatory item for the
> deposition.
>
> How can I keep the information that I used the Robetta calculated model?
>
> In advance thanks for your valuable answers.
>
> Cheers,
>
> Bernhard
>
> --
> Dr. Bernhard Loll
> Freie Universitaet Berlin
> Fachbereich Biologie, Chemie, Pharmazie
> Institut fuer Chemie und Biochemie
> AG Strukturbiochemie
> Takustr. 6
> D-14195 Berlin
> Germany
>
> Phone: +49 (0) 30 838-57348
> Fax:   +49 (0) 30 838-457348
> Email: l...@chemie.fu-berlin.de
> Homepage:
> http://www.bcp.fu-berlin.de/en/chemie/biochemie/research-groups/wahl-group/mitarbeiter/Dr__Bernhard_Loll.html/
>
> 
>
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-- 
Jan Abendroth
UCB BioSciences
Seattle / Bainbridge Island, WA, USA
home: jan.abendr...@gmail.com
work: jan.abendr...@ucb.com



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[ccp4bb] Postdoc position at USP (São Carlos, Brazil)

[Rafael Marques]

The Sérgio Mascarenhas Biophysics and Structural Biology Group, from IFSC/USP, 
is looking for exceptionally motivated and innovative candidates to carry out a 
postdoctoral fellowship in the Thematic Project “Septin filaments: structure, 
polymerization and action in pathologies” to develop a project using Cryo-EM as 
the main technique. In addition, negative staining electron microscopy, MALS 
and SAXS can also be used to determine the oligomerization state, shape and 
homogeneity of septin complexes.

Candidates must have a PhD degree obtained no more than 7 years ago and 
experience in protein purification.

Experience in Structural Biology and Cryo-EM are desirable, but not mandatory.

This opportunity is open to applicants of all nationalities.

Interested candidates should send, by February 25th, to the project 
coordinator, Richard C. Garratt (rich...@ifsc.usp.br ), the following documents 
for registration:

– A letter presenting your interest;
– A short CV, presenting academic background, publications, and information 
that proves your scientific experience;
- Letter of recommendation.


Best Regards

Rafael Marques da Silva
Mestrando em Física Biomolecular
Universidade de São Paulo

Bacharel em Ciências Biológicas
Universidade Federal de São Carlos

phone: +55 16 99766-0021

   "A sorte acompanha uma mente bem treinada"





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[ccp4bb] Survey on Data Standards and Databases in Molecular Biophysics

[Jan Dohnalek]

*Anonymous survey on Biophysical Data Standards and Accessibility*
We would like to know your experience and views on the current status and
needs for data standardization
and availability of databases for the individual techniques of molecular
biophysics.
You are invited to contribute to this world-wide survey and have your voice
heard!

Not all the biophysical data of your projects (spectroscopy, hydrodynamic
parameters, microscopy, thermodynamics, etc.) have standard data formats
and open access database,
respecting the FAIR principles (i.e. making the data Findable, Accessible,
Interoperable, and Reusable).

Within this HORIZON 2020 MOSBRI project (https://www.mosbri.eu) we want to
contribute toward standardizing biophysical data formats and archival.
Your anonymous answers will help us identify the priorities for data
standardization in non-structural molecular biophysics techniques.
Our further steps in the project will be directly influenced by your
answers. The survey results will be published.

Please, fill in your answers here (~10-15 minutes):

*https://forms.biocev.org/index.php/114374?lang=en
*

We appreciate your answers
The survey will close on 4 March 2022

*Feel free to contact us at mosbri-d...@ibt.cas.cz *

Jan Dohnálek & Jan Stránský
for the team of
Standards for data archiving & exploitation
MOSBRI

-- 
Jan Dohnalek, Ph.D
Institute of Biotechnology
Academy of Sciences of the Czech Republic
Biocev
Prumyslova 595
252 50 Vestec near Prague
Czech Republic

Tel. +420 325 873 758



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Re: [ccp4bb] Baculovirus expression system

[Artem Evdokimov]

There are several but if you discount the transfection based ones (i.e.
direct DNA, no virus at all) then the speed is roughly the same - about
four weeks from clone to process. FlashBac works a bit faster because it
avoids the use of ecoli to recombine the bacmid but the time savings is
about a week only.

As to yield - it is very protein specific and you do get many variables in
play including promoters, cell lines, media additives and so on

Artem

On Mon, Feb 7, 2022, 11:25 AM Srivastava, Dhiraj <
dhiraj-srivast...@uiowa.edu> wrote:

> Hi All
>  sorry for the question not related to crystallography. What is
> the baculovirus expression system that people use these days to get good
> yield in less time?
>
> Thank you
> Dhiraj
>
> --
>
> 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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Re: [ccp4bb] Baculovirus expression system

[Anshul Assaiya]

Please follow the link

https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/baculovirus-expression-system

On Mon, 7 Feb 2022, 21:54 Srivastava, Dhiraj, 
wrote:

> Hi All
>  sorry for the question not related to crystallography. What is
> the baculovirus expression system that people use these days to get good
> yield in less time?
>
> Thank you
> Dhiraj
>
> --
>
> 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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Re: [ccp4bb] Baculovirus expression system

[Antony Oliver]

Dear Dhiraj,

It may be perceived as “slow”, but we (still) use the Bac-to-Bac system from 
ThermoFisher (previously Invitrogen).
This coupled with the pFastBac, MultiBac or biGBac vector systems generally 
works well;  some proteins/complexes may express better in High 5 cells over 
Sf9/Sf21.

With regards,

Antony.


Antony W Oliver FHEA, PhD
Faculty Senior Research Fellow
Genome Damage and Stability Centre
Science Park Road
University of Sussex
Falmer, Brighton, BN1 9RQ





(office): +44 (0)1273 678349
(lab): +44 (0)1273 677512

antony.oli...@sussex.ac.uk; (he/him)
https://www.sussex.ac.uk/lifesci/oliverlab
https://tinyurl.com/aw-oliver
https://orcid.org/-0002-2912-8273
http://www.sussex.ac.uk/lifesci/internal/staff/support

From: CCP4 bulletin board  on behalf of "Srivastava, 
Dhiraj" 
Reply to: "Srivastava, Dhiraj" 
Date: Monday, 7 February 2022 at 16:24
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: [ccp4bb] Baculovirus expression system

Hi All
 sorry for the question not related to crystallography. What is the 
baculovirus expression system that people use these days to get good yield in 
less time?

Thank you
Dhiraj





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[ccp4bb] Baculovirus expression system

[Srivastava, Dhiraj]

Hi All
 sorry for the question not related to crystallography. What is the 
baculovirus expression system that people use these days to get good yield in 
less time?

Thank you
Dhiraj



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Re: [ccp4bb] PDB deposition of structure solved with a Robetta model

[Krieger, James M]

What do people think about depositing the Robetta model to somewhere like 
Zenodo (or maybe PDB-Dev) and getting an id from that?

Best wishes
James

On 7 Feb 2022, at 13:25, Loll, Bernhard  wrote:

Dear all,

I have recently solved a structure by molecular replacement with a search model 
calculated by the Robetta server.

I am in the process to deposit the coordinates. Now, I am wondering which 
information I should give on the starting model. Routinely, I would provide the 
the PDB code, which is a mandatory item for the deposition.

How can I keep the information that I used the Robetta calculated model?

In advance thanks for your valuable answers.

Cheers,

Bernhard

--
Dr. Bernhard Loll
Freie Universitaet Berlin
Fachbereich Biologie, Chemie, Pharmazie
Institut fuer Chemie und Biochemie
AG Strukturbiochemie
Takustr. 6
D-14195 Berlin
Germany

Phone: +49 (0) 30 838-57348
Fax:   +49 (0) 30 838-457348
Email: l...@chemie.fu-berlin.de
Homepage: 
https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.bcp.fu-berlin.de%2Fen%2Fchemie%2Fbiochemie%2Fresearch-groups%2Fwahl-group%2Fmitarbeiter%2FDr__Bernhard_Loll.html%2Fdata=04%7C01%7Ckriegerj%40PITT.EDU%7C0c5e9e4be2fb4616102808d9ea3d2c75%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637798371343719535%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000sdata=36vvt4WG4pb6wQGvVLNKPzP2iFfoYPi51fxYgMZwEuI%3Dreserved=0



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[ccp4bb] ReNaFoBiS/FRISBI/INSTRUCT-ERIC webinar

[CAVARELLI Jean (VIE)]

Dear All, 

You are invited to a ReNaFoBiS/FRISBI/INSTRUCT-ERIC webinar. 

When: March 1, 2022 04:00 PM Paris 
Topic: New Opportunities for Integrated Structural Biology at 4th generation 
synchrotron sources . 
Webinar Speaker : Dr Andrew THOMPSON (Synchrotron SOLEIL) 


Register in advance for this webinar: 
[ https://us06web.zoom.us/webinar/register/WN_unvGJZCVSOyJRXwHUY-AXg | 
https://us06web.zoom.us/webinar/register/WN_unvGJZCVSOyJRXwHUY-AXg ] 


After registering, you will receive a confirmation email containing information 
about joining the webinar. 

-- 
Andrew Thompson started his career at the SRS daresbury laboratory, working 
with John Helliwell, Colin Nave and Miroslav Papiz on the protein 
crystallography beamlines. 
He then moved to EMBL grenoble oustation, as part of a new collaboration 
between the ESRF and EMBL where he built and operated beamlines BM14 and ID29 
for anomalous phasing measurements in x-ray diffraction. After joining 
synchrotron SOLEIL in 2002, Andrew Thompson constructed and operated the 
Proxima1 facility, moving into a mangerial post in 2014. He is currently 
working on the Proxima1 beamline whilst preparing SOLEIL for the arrival of its 
first 300 kV cryo-electron microscope which is expected in early 2023. 
- 









- 
Jean Cavarelli 
Professor of Structural Biology 
"Structural biology of epigenetic targets" 
Department of Integrated structural biology 
IGBMC,UMR7104 CNRS-UNISTRA, INSERM U 1258 
phone : +33 (0)3 69 48 52 74 




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[ccp4bb] PDB deposition of structure solved with a Robetta model

[Loll, Bernhard]

Dear all,

I have recently solved a structure by molecular replacement with a 
search model calculated by the Robetta server.


I am in the process to deposit the coordinates. Now, I am wondering 
which information I should give on the starting model. Routinely, I 
would provide the the PDB code, which is a mandatory item for the 
deposition.


How can I keep the information that I used the Robetta calculated model?

In advance thanks for your valuable answers.

Cheers,

Bernhard

--
Dr. Bernhard Loll
Freie Universitaet Berlin
Fachbereich Biologie, Chemie, Pharmazie
Institut fuer Chemie und Biochemie
AG Strukturbiochemie
Takustr. 6
D-14195 Berlin
Germany

Phone: +49 (0) 30 838-57348
Fax:   +49 (0) 30 838-457348
Email: l...@chemie.fu-berlin.de
Homepage: 
http://www.bcp.fu-berlin.de/en/chemie/biochemie/research-groups/wahl-group/mitarbeiter/Dr__Bernhard_Loll.html/



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