Re: [ccp4bb] Phenix / Coot neutron queries.

[Paul Emsley]

On 20/06/2019 17:44, Jonathan Cooper wrote:
I am trying to refine a neutron structure for someone and I have come across a couple of things which I need 
help with.


I am struggling to get the occupancy refinement of the hydrogens/deuteriums on the N-terminal nitrogens to 
behave right. Some of them get deleted by readyset but the trick seems to be to call them hydrogen in the 
atom name field yet say they are D in the element symbol field. Is that the best way?  Also, readyset seems 
to delete the D's in D2O?


I would appreciate any tips on what is the best 'strategy' for refining with neutron data i.e. reciprocal- 
versus real-space or both, etc, because my R-free just seems to go up.


Also, if I do a real-space refine on a D2O molecule (DOD) in Coot it stretches the O-D bond length from 
around 1 to 1.3 Angstrom and the bond angle from ~110 to about 120 degrees so it seems to be picking-up 
wrong geometry info from somewhere.



Not helpful but related:

It has been a while since I looked at this, I recall that Coot and Phenix disagree about neutron-refinement 
restraints usage on a quite fundamental level which means they practically don't work together. (I'd like 
them to work together, but this issue has not reached the top of the todo list.)


Paul.



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Re: [ccp4bb] DNA or RNA

[Tri Ngo]

I think you could use Qubit.
https://www.thermofisher.com/us/en/home/industrial/spectroscopy-elemental-isotope-analysis/molecular-spectroscopy/fluorometers/qubit.html

On Thu, Jun 20, 2019 at 5:17 PM Reza Khayat  wrote:

> Hi,
>
>
> Sorry for the non-crystallography question. We have a protein complex with
> nucleic acid and would like to know if the nucleic acid is DNA or RNA. Is
> there a sensitive method for doing this where we don't need buckets of the
> sample? Thanks.
>
>
> Best wishes,
> Reza
> ​
> Reza Khayat, PhD
> Assistant Professor
> City College of New York
> Department of Chemistry
> New York, NY 10031
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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>



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[ccp4bb] Structural biologist to join the Structural Motility team at the Curie Institute Paris, France

[Houdusse-Juille Anne]

Job opening for a structural biologist to join the Structural Motility team at 
the Curie Institute Paris, France.

We are looking for a post-doctoral fellow to join the team Structural Motility 
at the Curie Institute (Paris Center) directed by Anne Houdusse.

The Structural Motility team at the Institut Curie has gathered important 
structural insights on how force generated by molecular motors can power 
cellular processes in human health and disease. We combine chemical biology and 
optogenetics approaches to test these insights and understand how molecular 
motors produce force, how their activity is regulated and how they are 
recruited to their cellular targets. Many of these motors are also involved in 
human pathologies and they are thus good targets for new therapies which we are 
helping to develop.
The post-doctoral fellow we will hire will coordinate these approaches and 
perform research to gain more structural insights concerning a molecular motor 
that is a target against cancer. We are looking for an expert in biochemical, 
crystallogenesis and structural determination studies. The post-doctoral fellow 
will also gain expertise in functional and cellular studies.
A solid experience in crystallization and X-ray structural determination is 
required. Experience in the production and purification of recombinant proteins 
is a plus but we are ready to train a dynamic and motivated candidate.

If you are interested, please send a CV and a letter of motivation as well as 
letters of recommendation of your previous employers.

Contact : Anne Houdusse (anne.houdu...@curie.fr)
https://science.institut-curie.org/research/multiscale-physics-biology-chemistry/umr144-subcellular-structure-and-cellular-dynamics/team-houdusse/

   Recent publications
Robert-Paganin et al, Nat Commun. In press.
Robert-Paganin et al, Nat Commun. 9, 4019, 2018.
Planelles-Herrero VJ, Hartman JJ, Robert-Paganin J, Malik FI, Houdusse A. 
Mechanistic and Structural Basis for Activation of Cardiac Myosin Force 
Production by Omecamtiv Mecarbil. Nat. Commun. 8, 190, 2017.
Yu I-M*, Planelles-Herrero VJ*, Sourigues Y, Moussaoui D, Sirkia H, Kikuti C, 
Stroebel D, Titus MA, Houdusse A. Myosin 7 and its Adaptors Link Cadherins to 
Actin. Nat Commun. 8, 15864, 2017.
Houdusse A, Sweeney HL. How myosin generates force on actin filaments. Trends 
Biochem Sci. 41, 989-97, 2016.
Sweeney HL and Houdusse A, Myosin VI rewrites the rules for myosin motors, 
Cell, 141, 573-82, 2010.
Sweeney HL and Houdusse A. Structural and Functional Insights into the Myosin 
Motor Mechanism, Annu Rev Biophys. 39, 539-57, 2010.


Anne Houdusse-Juillé, Directeur de Recherche CNRS
Institut Curie - UMR 144
Group Leader -- Structural Motility Team
26 rue  d'Ulm
F-75248 Paris cedex 05

Tel: +33-1-5624-6395
FAX: +33-1-5624-6319
E-mail: anne.houdu...@curie.fr
https://goo.gl/aUY51R







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[ccp4bb] Phenix / Coot neutron queries.

[Jonathan Cooper]

I am trying to refine a neutron structure for someone and I have come across a 
couple of things which I need help with.
I am struggling to get the occupancy refinement of the hydrogens/deuteriums on 
the N-terminal nitrogens to behave right. Some of them get deleted by readyset 
but the trick seems to be to call them hydrogen in the atom name field yet say 
they are D in the element symbol field. Is that the best way?  Also, readyset 
seems to delete the D's in D2O?
I would appreciate any tips on what is the best 'strategy' for refining with 
neutron data i.e. reciprocal- versus real-space or both, etc, because my R-free 
just seems to go up.
Also, if I do a real-space refine on a D2O molecule (DOD) in Coot it stretches 
the O-D bond length from around 1 to 1.3 Angstrom and the bond angle from ~110 
to about 120 degrees so it seems to be picking-up wrong geometry info from 
somewhere.



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Re: [ccp4bb] DNA or RNA

[Aaron Thompson]

Hi Reza,

I'm not sure if this is sensitive enough, but Stains-All might be worth a
try.

Cationic carbocyanine dye used for differential staining of nuclei acids
and proteins with RNA staining blue/purple, DNA staining blue, and proteins
staining red.

https://www.abcam.com/stains-all-cationic-carbocyanine-dye-ab146278.html

Aaron

On Thu, Jun 20, 2019 at 3:17 PM Reza Khayat  wrote:

> Hi,
>
>
> Sorry for the non-crystallography question. We have a protein complex with
> nucleic acid and would like to know if the nucleic acid is DNA or RNA. Is
> there a sensitive method for doing this where we don't need buckets of the
> sample? Thanks.
>
>
> Best wishes,
> Reza
> ​
> Reza Khayat, PhD
> Assistant Professor
> City College of New York
> Department of Chemistry
> New York, NY 10031
>
> --
>
> 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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Re: [ccp4bb] DNA or RNA

[Keller, Jacob]

Hi Reza,

What about seeing whether RNAse and DNAse incubations kill the complex?

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
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From: CCP4 bulletin board  On Behalf Of Reza Khayat
Sent: Thursday, June 20, 2019 6:16 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] DNA or RNA


Hi,



Sorry for the non-crystallography question. We have a protein complex with 
nucleic acid and would like to know if the nucleic acid is DNA or RNA. Is there 
a sensitive method for doing this where we don't need buckets of the sample? 
Thanks.



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



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[ccp4bb] DNA or RNA

[Reza Khayat]

Hi,


Sorry for the non-crystallography question. We have a protein complex with 
nucleic acid and would like to know if the nucleic acid is DNA or RNA. Is there 
a sensitive method for doing this where we don't need buckets of the sample? 
Thanks.


Best wishes,
Reza

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



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Re: [ccp4bb] Alternate conformations in coot

[Paul Emsley]

On 20/06/2019 10:50, Horrell, Sam wrote:


I've been having some trouble with double conformations in coot lately. Real space refinement acts on both 
of the residues at once so both conformations just end up in pretty much the same place if I try and use the 
weighted map or the weighted difference map. 


Known bug - the refinement was improved quite a lot recently but I missed this issue. On the list to fix for 
0.8.9.3. Sorry for the inconvenience.


Regards,

Paul.



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[ccp4bb] Post-doctoral Position at IGBMC (Strasbourg, France)

[Isabelle BILLAS MASSOBRIO]

Dear colleagues,

A post-doctoral position is available to study the mechanistic role of 
transcription factors in hematopoiesis and leukemogenesis at the structural 
level in the laboratory of Susan Chan and Philippe Kastner, at the Institut de 
Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) in Strasbourg, 
France (http://www.igbmc.fr/research/department/2/team/18/) in collaboration 
with the Department of Integrated Structural Biology.

The IGBMC is a component institute of the CERBM (European Centre for Research 
in Biology and Medicine) and one of the leading centres in biomedical research 
in France and Europe. It is well equipped for molecular, cellular and 
structural biology, as well as genetic and animal experimentation. The 
department of Integrated Structural Biology is located in the new Centre for 
Integrative Biology (CBI), which is part of the European distributed Structural 
Biology Infrastructure (Instruct) and is well equipped for structural 
investigations using state-of-the-art X-ray diffraction equipment and cryo 
electron microscopes (Titan Krios and Polara microscopes).

The project will aim at unveiling the architecture of transcriptional complexes 
with a multipronged structural and functional approach. This project will 
require the production, characterization and structural investigation of 
transcription factor-associated complexes. To achieve this goal, a range of 
techniques encompassing molecular biology, biochemistry and biophysical 
characterization, will be employed. The Postdoctoral Research fellow will 
benefit from access to the Structural Biology and Genomics platform at IGBMC 
(cloning, purification, crystallization).

Candidates must have a Ph.D. degree, a keen interest in structural biology, and 
should enjoy working as part of an interdisciplinary team.  They should have a 
background in at least one of the following areas: molecular biology; 
biochemistry, in particular protein expression and purification; biophysics;  
X-ray crystallography; cryo electron microscopy. We welcome highly qualified 
and motivated individuals, with a recently obtained PhD in structural biology 
and first author publications in peer-reviewed international journals, who can 
work easily in a multi-lab consortium. This position is available immediately 
and is funded for two years.

Please send a detailed CV with list of publications, a letter of motivation, 
and the names of three references to Susan Chan and Philippe Kastner 
(s...@igbmc.fr).


[bandeau signature_final]



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[ccp4bb] Team Leader and Fellowship Opportunities at Institute of Cancer Research

[Laurence Pearl]

The Institute of Cancer Research, London – Division of Structural Biology
Team Leader Positions & Independent Fellowship opportunities
The ICR is committed to attracting and developing the best minds in the world 
to join us in our mission – to make the discoveries that defeat cancer
The Institute of Cancer Research, London, is one of the world’s most 
influential cancer research organisations, with an outstanding record of 
achievement dating back more than 100 years. We provided the first convincing 
evidence that DNA damage is the basic cause of cancer, laying the foundation 
for the now universally accepted idea that cancer is a genetic disease. Today, 
we are world leaders in discovering new-targeted cancer drugs, identifying new 
cancer genes and developing new forms of precision radiotherapy.
Under the leadership of our Chief Executive and President, Professor Paul 
Workman FRS, The Institute of Cancer Research (ICR) is ranked as the UK’s 
leading higher education institution for the quality and impact of its 
research. Together with our partner The Royal Marsden NHS Foundation Trust, we 
are rated in the top five centres for cancer research and treatment worldwide. 
The ICR is committed to attracting and developing the best minds in the world 
to join us in our mission – to make the discoveries that defeat cancer.
Team Leader positions
As part of a programme of expansion of the Division of Structural Biology, we 
wish to establish three new research teams at the Institute’s Chester Beatty 
Laboratories in Chelsea, Central London. We are interested in established 
investigators, for whom permanent Faculty positions are available, and in 
emerging researchers able to attract externally-funded Personal Fellowships, 
for whom we will provide mentoring, and a generous support package and 
transparent review process.
Reflecting the Institute’s mission, we are looking for researchers whose 
interests inform our understanding of the origins, development and treatment of 
cancer. Current areas of interest include signal transduction, genome 
stability, transcription regulation, RNA processing, molecular chaperones, 
targeted protein degradation, and structure-based drug design.
The Division is exceptionally well equipped for modern structural biology, with 
excellent managed facilities for protein production, biophysical analysis, 
crystallisation and X-ray diffraction, and computation, as well as Techni T12 
and F20 cryo-electron microscopes, and a state-of the-art FEI Glacios/Falcon 3. 
The Division also has a 30% share of a Krios/K3 cryoEM facility at the Crick 
Institute, and rolling allocations of cryoEM time at the eBIC national 
facility, and X-ray diffraction time at the Diamond, ESRF and Soleil 
synchrotrons.
To apply online for Team Leader positions, please click on this 
link.
 This will re-route you to the ICR’s Web Recruitment System, where you will 
need to register for an account (if you have not already) and log in. Along 
with completing the online application form, you will be asked to attach the 
following documents and failure to do so will mean your application cannot be 
considered on this occasion:
•   Full CV
•   Lists of major publications, achievements, research grants, 
distinctions.
•   Covering letter including the names and contact details of three 
academic referees
•   Research plan (five to six pages outlining your current research 
interests and research programme for the next 5 years)
For informal enquiries, please contact the Head of Division, Professor Laurence 
Pearl FRS – laurence.pe...@icr.ac.uk
The Closing date for Team Leader applications is15th July 2019
Fellowship positions
The ICR is proactively seeking candidates who can be supported in making 
applications for personal fellowships provided by key fellowship schemes across 
the UK such as CRUK, Wellcome, MRC, etc.  ICR’s Research Operations Team will 
support the candidates in drafting applications to the major funding bodies. 
The salary component will be based on ICR’s own CDF scale. ICR will offer an 
additional support package to researchers with personal fellowships of a PhD 
studentship and a 3-year post-doctoral position with consumables paid for from 
ICR General Funds.
For informal enquiries, please contact the Head of Division, Professor Laurence 
Pearl FRS – laurence.pe...@icr.ac.uk
We are particularly keen to hear from women and members of minority ethnic 
groups who are currently under-represented in these positions








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Re: [ccp4bb] RAMACHANDRAN outlier of Thr

[Robbie Joosten]

Hi Shijun,

Yes there are differences in Ramachandran validation implementations. Just look 
at where your supposed outlier lies on the Ramachandran plot. If it is close to 
the edge of the distribution, I wouldn't worry about it.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> ???
> Sent: Thursday, June 20, 2019 10:24
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] RAMACHANDRAN outlier of Thr
> 
> Dear all
> 
>  The problem is when I check RAMACHANDRAN outlier with coot, it shows
> zero, while it become one Thr outlier in phenix.vadition. so I am confusing
> about the standard of RAMACHANDRAN outlier in coot and
> phenix.validation, any difference between them? Thanks
> 
> yours
> 
> shijun
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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[ccp4bb] Project manager in crystallography (M/F)

[Linda Miallau]

NovAlix is hiring a structural biologist, please see the add below:



NovAliX is a company specialized in external research (medicinal chemistry,
protein crystallography, process R). NovAliX offers a complete range of
services in the field of research and development of small molecules. The
company has a team of 100 scientists.

The position is permanent and based in Saclay, Essonne (South of
Paris-France).



You will join our 7-membered structural biology insourced team located on
the Synchrotron SOLEIL to manage projects for our client in the field of
structural biology. Your work will consist in:

- Conducting crystallographic projects from bibliographic work to
structure determination, as well as project follow-up, clients reporting,
drafting procedures and/or reports.

- Managing and supervising a team of research associates.

You will be in charge of *protein production and purification* from
different expression systems, X-ray diffraction data collection &
processing, structure determination of proteins of interest and of
protein-ligand complexes.



You should have a PhD in crystallography with ca. 4-6 years of experience
in modern Crystallography techniques (preferentially experienced in the
life science industry) during which you have deepened and widened your
practical and theoretical knowledge in the field of construct design,
protein biochemistry and crystallography. A good knowledge of software
packages employed in protein crystallography is a must. Additional
experience in molecular biology and/or insect cells culture, membrane
proteins and/or characterization of protein/ligand complexes would be an
asset.

We are seeking a person who speaks fluently English and French, who is
passionate about structural biology and who has a keen sense of
responsibility as well as being a committed team player. The candidate will
have a rigorous and organized attitude to work with excellent supervisory
and reporting skills.



Please send your questions/application (CV, research statement and
references) by email to:

*car...@novalix.com *



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[ccp4bb] RAMACHANDRAN outlier of Thr

[张士军]

Dear all

 The problem is when I check RAMACHANDRAN outlier with coot, it shows zero, 
while it become one Thr outlier in phenix.vadition. so I am confusing about the 
standard of RAMACHANDRAN outlier in coot and phenix.validation, any difference 
between them? Thanks

yours

shijun



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