Re: [ccp4bb] Searching similar local structural conformations

[Rigden, Dan]

Dear Lei


You can use ASSAM for this


http://27.126.156.175/assam/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394286/


In the past I've also used SPASM locally for this

http://xray.bmc.uu.se/usf/spasm.html

but I think you'll need to generate your own up to date database to search.


Best wishes

Dan



From: CCP4 bulletin board  on behalf of Zheng, Lei 

Sent: 08 January 2020 15:57:23
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Searching similar local structural conformations

Dear CCP4ers,

We identify a potential ion binding site formed by four residues in a 
structure. I want to search if any other structures have a similar local 
residual geometry. Is there any programs to perform such a searching? For 
example, to search in Protein Data Bank using coordinates of the binding site 
residues? I appreciate your suggestions.

Happy New Year!
Lei





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Re: [ccp4bb] Protein concentration for the initial crystallisation trials

[Newman, Janet (Manufacturing, Parkville)]

Hi,

Another way of estimating a starting protein concentration is to watch your 
concentration process – if your protein is in a spin concentrator (with an 
appropriate membrane cutoff size  say ~ [MW protein]/3) and is losing volume 
really quickly then keep going. As soon as the concentration starts slowing 
down try that concentration. Actually, you should really follow the experience 
of the Oxford SGC where they always set up three drop ratios of protein to 
reservoir solution – 1:2, 1:1 and 2:1.

Cheers, Janet

From: CCP4 bulletin board  On Behalf Of Edward Snell
Sent: Thursday, 9 January 2020 3:52 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Protein concentration for the initial crystallisation 
trials

Hi Armando,

I echo Rodger’s advice at 10 mg/ml to start. Our high-throughput 
crystallization lab has a FAQ page that notes this 
https://hwi.buffalo.edu/high-throughput-crystallization-center/hts-faqs/ but we 
absolutely recommend looking at conditions where the precipitant concentration 
varies AND doing a screen with a different protein concentration if sample is 
available. Both have considerable impact on outcome and the screens we use are 
designed to provide information on this if they are interpreted correctly. 
There are a lot of internal references available at 
https://hwi.buffalo.edu/high-throughput-crystallization-center/crystallization-research/.
 I would recommend the “What’s in a drop?” paper.

If there are any homologous proteins that have been crystallized than those 
conditions can be a good starting guide. There are some proteins that are far 
more soluble than typical and can have concentrations almost an order of 
magnitude greater and the occasional on an order of magnitude less. I don’t 
remember an absolute study on this but I’m sure there must be as I vaguely 
remember advice that was size related, smaller proteins requiring higher 
concentration, larger ones less. This may jog someone’s memory to provide the 
reference.

Forgive me for a blatant advertisement, but there is a very successful 
crystallization screening service at http://getacrystal.org
that screens a large array of conditions in a manner to extract this kind of 
information from them, provides visual, SONICC and UV imaging, and can study 
the process at multiple temperatures (very useful from a solubility point of 
view and preserving samples that may be more transient).  We hope to implement 
MARCO (https://marco.ccr.buffalo.edu/) very soon (which has to be added to the 
reference list – we slipped up there) so you don’t even need to look at all the 
images. This is a machine vision system we have been developing with many 
collaborators – it works! 
(https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0198883).

As Janet Newman so elegantly said recently, may your New Year Resolutions be 
high.

Best,

Eddie


Edward Snell Ph.D.

Director of the NSF BioXFEL Science and Technology Center
President and CEO Hauptman-Woodward Medical Research Institute
BioInnovations Chaired Professorship, University at Buffalo, SUNY
700 Ellicott Street, Buffalo, NY 14203-1102
hwi.buffalo.edu
Phone:   (716) 898 8631 Fax: (716) 898 8660
Skype:eddie.snell Email: 
esn...@hwi.buffalo.edu
Webpage: https://hwi.buffalo.edu/scientist-directory/snell/
[cid:image002.png@01D5C6D4.DD9518C0]
Heisenberg was probably here!

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger 
Rowlett
Sent: Wednesday, January 8, 2020 11:29 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Protein concentration for the initial crystallisation 
trials

I usually set a partial screen, maybe 24-48 conditions. If less than half the 
wells have precipitate, double protein concentration. If most have precipitate, 
maybe reduce protein or halve concentration of screen reagents. I usually start 
at 10 mg/mL or so. You can conveniently change protein conc. by manipulating 
protein/screen volume ratio.
__
Roger Rowlett

On Wed, Jan 8, 2020, 11:16 AM Armando Albert 
mailto:xalb...@iqfr.csic.es>> wrote:
Dear all,
I was wondering how to guess the optimal protein concentration for the initial 
crystallisation trials. Is there any trick or assay other than the classic PCT 
from Hampton?
Armando



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[ccp4bb] Research Scientist/Engineer Assistant – Crystallography: in INSTITUTE for PROTEIN DESIGN @Seattle

[StrBio]

Research Scientist/Engineer Assistant – Crystallography


*Opening:* *Current*

The UW Institute for Protein Design currently has an outstanding
opportunity for a Research Scientist Assistant to support peptide and
protein crystallography efforts for the IPD’s Structural Biology Core
(SBC).  This person will be assigned work under general guidance and
receive instruction on specific assignment objectives, complex features,
and possible solutions. Guidance on unusual problems will be provided by
IPD Faculty, other UW Faculty, or other experts in biophysical
characterization and work shall be reviewed for application of sound
professional judgment.

The Research Scientist Assistant – SBC will interface directly with members
of other IPD Core Laboratories as well as graduate students and
postdoctoral fellows in IPD Faculty Laboratories. Research activities will
involve setup of crystallization trays, screening for crystal formation and
growth using microscopy, operation of X-ray generation sources, and
eventually training in data collection and solving structures.  The RSA SBC
will grow to be an expert in protein and peptide x-ray crystallography and
will therefore be of assistance in optimization of crystallization
conditions and support of crystallography needs for the IPD. With the
gaining of expertise, high throughput robotics, maintenance and operation
of x ray sources and independent operation in crystallography projects.

In this role, ~40% of the effort will be dedicated to the setup and
monitoring of crystallography trays.

Another ~20% of effort will be dedicated to maintenance and operation of
liquid handling robotics.

The remaining ~40% of effort will, eventually, be dedicated to the
maintenance and operation of x-ray generating sources for x-ray diffraction
of peptides and proteins.

*Minimum Requirements:*

   - Bachelors’s Degree in Biochemistry, Biology or similar + less than 3
   months of experience in related field.
   - The Research Scientist Assistant-SBC is devoted primarily to
   scientific research and requires a B. Sc. in a biology-related field,  with
   less than 3 months of experience in characterization of protein. Candidates
   must be capable of applying standardized scientific procedures and
   techniques to assignments of limited complexity, involving potentially
   conflicting design requirements.

   *Desired:*
   An ideal Research Scientist Assistant – SBC candidate will be someone
   who (i) has had experience in a laboratory setting during the undergraduate
   degree obtention, (ii) will use their knowledge gained in their
   undergraduate degree program to apply fundamental concepts, practices and
   procedures, (iii) follows procedures for small projects and/or major
   project tasks which may last years under immediate supervision, and
   effectively manages them under guidance and direction from project staff;
   interfaces with investigator peers, (iv) can provide timely and
   professional scientific services to a number of internal collaborators on
   approximately 2-3 different projects, (v) can perform tasks and methods as
   directed, (vi) and enjoys interacting with other scientists in a highly
   collaborative and fast-paced work environment.

Link:

> https://www.ipd.uw.edu/employment/
>



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[ccp4bb] nVidia 3D Vision2 glasses

[Patricia Borges]

Dear all,

Does anyone knows any alternative to the nVidia 3D Vision2 glasses for a
Ubuntu workstation, since these are at the moment discontinued?

Thanks a lot for the help,
Best regards
Patricia



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Re: [ccp4bb] Searching similar local structural conformations

[Emilia C. Arturo (Emily)]

Lei,

The DeGrado lab developed a tool that would do just what you seek to do and
could function as a PyMOL plugin. I played with it a few years ago after I
found an interesting cation-pi sandwhich in my structure. I e-mailed then
with the author, hoping to link the tool to the entire current PDB
inventory, but then had to move on to another project, so am not certain
how updated it is now.  Have a look at the tool and documentation here:
http://degradolab.org/suns/ It is reported in 2014 by Gonzalez et al, here:
https://www.ncbi.nlm.nih.gov/pubmed/25079944

Regards,
Emily.

On Wed, Jan 8, 2020 at 7:57 AM Zheng, Lei  wrote:

> Dear CCP4ers,
>
>
>
> We identify a potential ion binding site formed by four residues in a
> structure. I want to search if any other structures have a similar local
> residual geometry. Is there any programs to perform such a searching? For
> example, to search in Protein Data Bank using coordinates of the binding
> site residues? I appreciate your suggestions.
>
>
>
> Happy New Year!
>
> Lei
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>


-- 
"Study as if you were going to live forever; live as if you were going to
die tomorrow." - Maria Mitchell

"I'm not afraid of storms for I'm learning to sail my ship."  - Louisa May
Alcott



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[ccp4bb] PostDoctoralPosition@UCIrvine

[Celia Goulding]

The Goulding lab in the Department of Molecular Biology and Biochemistry at the 
University of California at Irvine seeks to recruit an outstanding postdoctoral 
scientist with experience and interest in structural biology and biochemistry 
of protein complexes. The Goulding lab focuses on iron uptake in Mycobacterium 
tuberculosis. This position provides the opportunity for broad training in 
structural biology, metalloprotein biochemistry, kinetics, spectroscopy, and 
microbiology.

The University of California at Irvine campus is located on the beautiful 
Southern Californian coast-line approximately five miles from vibrant Newport 
Beach and Crystal Cove.   It is also approximately 40 miles from both Los 
Angeles and San Diego.  The surrounding areas offer affordable rental housing 
with a short walk/ride to campus, the beach and nightlife.

Candidates must have their Ph.D. by the beginning date of the appointment in 
Biological Chemistry or a related discipline (Chemistry, Biochemistry, 
Molecular Biology and Biophysics, Microbiology, Pharmaceutical Sciences, 
Biochemical, and Biomedical engineering). The successful candidate will have 
strong experience in molecular biology, protein expression, purification, 
crystallization, and functional analysis. Training in X-ray crystallographer is 
desirable. Opportunities will exist for involvement in specific projects and 
co-authorship of manuscripts, and requires a two-year commitment.  

The salary will follow NIH guidelines for post-doctoral fellows and depends on 
previous experience.

To apply, please send curriculum vitae and the names of three references to: 
celia.gould...@uci.edu.  Review of applications will begin immediately and will 
continue until the position is filled. 

The University of California is an equal opportunity affirmative action 
employer.  Women and minorities are encouraged to apply.



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Re: [ccp4bb] Protein concentration for the initial crystallisation trials

[Edward Snell]

Hi Armando,

I echo Rodger’s advice at 10 mg/ml to start. Our high-throughput 
crystallization lab has a FAQ page that notes this 
https://hwi.buffalo.edu/high-throughput-crystallization-center/hts-faqs/ but we 
absolutely recommend looking at conditions where the precipitant concentration 
varies AND doing a screen with a different protein concentration if sample is 
available. Both have considerable impact on outcome and the screens we use are 
designed to provide information on this if they are interpreted correctly. 
There are a lot of internal references available at 
https://hwi.buffalo.edu/high-throughput-crystallization-center/crystallization-research/.
 I would recommend the “What’s in a drop?” paper.

If there are any homologous proteins that have been crystallized than those 
conditions can be a good starting guide. There are some proteins that are far 
more soluble than typical and can have concentrations almost an order of 
magnitude greater and the occasional on an order of magnitude less. I don’t 
remember an absolute study on this but I’m sure there must be as I vaguely 
remember advice that was size related, smaller proteins requiring higher 
concentration, larger ones less. This may jog someone’s memory to provide the 
reference.

Forgive me for a blatant advertisement, but there is a very successful 
crystallization screening service at http://getacrystal.org
that screens a large array of conditions in a manner to extract this kind of 
information from them, provides visual, SONICC and UV imaging, and can study 
the process at multiple temperatures (very useful from a solubility point of 
view and preserving samples that may be more transient).  We hope to implement 
MARCO (https://marco.ccr.buffalo.edu/) very soon (which has to be added to the 
reference list – we slipped up there) so you don’t even need to look at all the 
images. This is a machine vision system we have been developing with many 
collaborators – it works! 
(https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0198883).

As Janet Newman so elegantly said recently, may your New Year Resolutions be 
high.

Best,

Eddie


Edward Snell Ph.D.

Director of the NSF BioXFEL Science and Technology Center
President and CEO Hauptman-Woodward Medical Research Institute
BioInnovations Chaired Professorship, University at Buffalo, SUNY
700 Ellicott Street, Buffalo, NY 14203-1102
hwi.buffalo.edu
Phone:   (716) 898 8631 Fax: (716) 898 8660
Skype:eddie.snell Email: esn...@hwi.buffalo.edu
Webpage: https://hwi.buffalo.edu/scientist-directory/snell/
[cid:image001.png@01D5C619.F8914650]
Heisenberg was probably here!

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger 
Rowlett
Sent: Wednesday, January 8, 2020 11:29 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Protein concentration for the initial crystallisation 
trials

I usually set a partial screen, maybe 24-48 conditions. If less than half the 
wells have precipitate, double protein concentration. If most have precipitate, 
maybe reduce protein or halve concentration of screen reagents. I usually start 
at 10 mg/mL or so. You can conveniently change protein conc. by manipulating 
protein/screen volume ratio.
__
Roger Rowlett

On Wed, Jan 8, 2020, 11:16 AM Armando Albert 
mailto:xalb...@iqfr.csic.es>> wrote:
Dear all,
I was wondering how to guess the optimal protein concentration for the initial 
crystallisation trials. Is there any trick or assay other than the classic PCT 
from Hampton?
Armando



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Re: [ccp4bb] Protein concentration for the initial crystallisation trials

[Tim Gruene]

Dear Armando,

in case you have enough material to spare, I would use a concentrator to 
create a saturated solution, i.e. concentrate until it precipitates. Measure 
the concentration of the saturated solution, i.e., supernatant without 
disturbing the solution with the precipitate.

You can start crystallisation trials at 70-90% of this concentration.

Best,
Tim

On Wednesday, January 8, 2020 5:16:31 PM CET Armando Albert wrote:
> Dear all,
> I was wondering how to guess the optimal protein concentration for the
> initial crystallisation trials. Is there any trick or assay other than the
> classic PCT from Hampton? Armando
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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signature.asc
Description: This is a digitally signed message part.

Re: [ccp4bb] Protein concentration for the initial crystallisation trials

[Roger Rowlett]

I usually set a partial screen, maybe 24-48 conditions. If less than half
the wells have precipitate, double protein concentration. If most have
precipitate, maybe reduce protein or halve concentration of screen
reagents. I usually start at 10 mg/mL or so. You can conveniently change
protein conc. by manipulating protein/screen volume ratio.

__
Roger Rowlett

On Wed, Jan 8, 2020, 11:16 AM Armando Albert  wrote:

> Dear all,
> I was wondering how to guess the optimal protein concentration for the
> initial crystallisation trials. Is there any trick or assay other than the
> classic PCT from Hampton?
> Armando
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] Protein concentration for the initial crystallisation trials

[Armando Albert]

Dear all, 
I was wondering how to guess the optimal protein concentration for the initial 
crystallisation trials. Is there any trick or assay other than the classic PCT 
from Hampton?
Armando
 


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Re: [ccp4bb] Searching similar local structural conformations

[Reza Khayat]

?Hi Lei,


Rosetta uses something very similar to this for designing proteins that bind to 
ligands/proteins. Perhaps look there.


Best wishes,
Reza


Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031

From: CCP4 bulletin board  on behalf of Zheng, Lei 

Sent: Wednesday, January 8, 2020 10:57 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] [ccp4bb] Searching similar local structural conformations

Dear CCP4ers,

We identify a potential ion binding site formed by four residues in a 
structure. I want to search if any other structures have a similar local 
residual geometry. Is there any programs to perform such a searching? For 
example, to search in Protein Data Bank using coordinates of the binding site 
residues? I appreciate your suggestions.

Happy New Year!
Lei





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[ccp4bb] Searching similar local structural conformations

[Zheng, Lei]

Dear CCP4ers,

We identify a potential ion binding site formed by four residues in a 
structure. I want to search if any other structures have a similar local 
residual geometry. Is there any programs to perform such a searching? For 
example, to search in Protein Data Bank using coordinates of the binding site 
residues? I appreciate your suggestions.

Happy New Year!
Lei





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[ccp4bb] Reminder - PDBe workshop: Making the most of PDB data with PDBe’s new graph database

[David Armstrong]

Are you looking to use PDB data more effectively to answer complex 
scientific questions? Do you have experience of accessing data 
programmatically, but want to ask more complex questions? Then you will 
be interested in our EBI training workshop on accessing PDBe and PDBe-KB 
data using our new graph database.



This workshop covers the use of the PDBegraph database 
to extract data for solving 
complex structural biology queries. It will introduce the PDBe graph 
database and how to write Cypher queries to retrieve data of interest. 
Workshop participants will be able to use the graph database to explore 
data relevant to their own research with support and guidance from the 
development team at PDBe.



For more information and to register, please visit 
www.ebi.ac.uk/training/events/2020/mining-pdbe-and-pdbe-kb-using-graph-database 
.



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] 3 PhD studentships in the Centre for Structural Medicine, QMUL

[Vidya Darbari]

Could you please forward the following PhD studentship opportunities to 
suitable candidates?


The newly formed “Centre for Structural Medicine” (joint between the 
Schools of Biological and Chemical Sciences and Medicine and Dentistry) 
is seeking PhD applicants for their fully funded mini Centre for 
Doctoral Training (CDT) on Overcoming drug-resistant microbial infection 
– Targeting the power of Molecular Machines to start in September 2020. 
Our Centre incorporates 13 academics and their research groups (each 
student will be jointly supervised).


Deadline: 31st January 2020

The PhD students will investigate the architecture and function of 
molecular machines essential for microbial infection. These will aim to 
pinpoint novel and functionally critical protein-protein interactions, 
evolve/screen for biological therapeutics that inhibit these 
interactions and thus discover new lead antimicrobials. The mini-CDT 
will be divided into the following themes: molecular machines important 
(i) pre-infection, (ii) during infection and (iii) post-infection.


Funding: Three studentships are available. The studentships are open to 
UK/EU applicants and are funded by Queen Mary University of London. The 
funding will cover tuition fees, and provide an annual tax-free 
maintenance allowance for 3 years at the Research Council rate (£17,009 
in 2019/20).


Informal enquries can be sent to Dr Ewan Main (e.m...@qmul.ac.uk 
). Formal applications should be submitted 
through the online form by the stated deadline. Applicants should 
identify their intended funding source as 'CfSM mini-CDT' within the 
online application form to ensure it is clear that they wish to be 
considered for these studentships.


Further information available from 
https://www.qmul.ac.uk/sbcs/postgraduate/phd-programmes/projects/display-title-762256-en.html


Best Regards
Vidya Darbari.



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[ccp4bb] Study Weekend 2020 live stream

[David Waterman]

Hi everybody,

For those wishing to view the CCP4 Study Weekend live stream, please click
here: https://ukri.zoom.us/j/195886424

We are about to start.

Cheers
-- David



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[ccp4bb] CCP4 Study Weekend live stream link

[Karen McIntyre - UKRI STFC]

For those wanting to watch the CCP4 Study Weekend 2020 via the live stream the 
link is below:

Please click the link below to join the webinar:
https://ukri.zoom.us/j/195886424

On the CCP4 website people will be connected to the conference both days, 8th 
and 9th January

Regards

Karen McIntyre
CCP4 Project Administrator
Science and Technology Facilities Council
karen.mcint...@stfc.ac.uk
01235 44 5790


[cid:image002.png@01D5C601.F3577640]

**Please note that I only work mornings until 1.30pm**




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[ccp4bb] Open position at EMBL Grenoble - Scientific Expert for Eukaryotic Protein Production

[Marco MARCIA]

Dear all
I am writing to kindly remind you that the EMBL Grenoble opening for a 
Scientific Expert for Eukaryotic Protein Production is closing one week 
from now.

Closing date: Jan 15th 2020.
You can read more about the position and submit your application at:
https://www.embl.de/jobs/searchjobs/index.php?ref=GR00141=1

Regards
Marco



--
Dr. Marco MARCIA
Group Leader
EMBL Grenoble
71 Avenue des Martyrs, room 254
38042 Grenoble Cedex 09
France
phone (lab): 0033-(0)476207634
phone (office): 0033-(0)476207759
fax: 0033-(0)476207199
email: mmar...@embl.fr
web: https://embl.fr/research/unit/marcia/



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