Re: [ccp4bb] Selecting best chain for NCS

[Robbie Joosten]

Hi Chetan,

Unless the model is horrendously far away from the final result, I would do the 
following instead of the chain copying:
- Start from chain A with NCS ghosts in COOT and go through the model residue 
by residue. Refine 3-residue windows. If you see NCS deviation. Cycle through 
the other chains and NCS match things unless the maps clearly tell you 
otherwise.
- After the first ~200 residues, move to the difference density peaks. Fix what 
you can fix.
- Refine the model in Refmac and with local NCS.
- Go to COOT and repeat with the next residues until you have seen the entire 
model.

If you keep notes of the things you are unsure of you can revisit those 
residues later. With hotkeys in COOT and some practice, you can do a COOT 
session in about an hour. You'll see it will get easier soon.
To give your model a first kick you can also try pdb-redo to see if if can 
improve you model stats a bit. You never know with early models, but it doesn't 
take much time to try.

HTH,
Robbie

PS 8 is a nice number, are you sure your space group is correct?

On 4 Dec 2018 07:33, Chetan A  wrote:
Hello All,
I am trying to refine some protein structure and right now my structure's 
R-free is not coming down from 37% even the R-work is lowering in each round of 
refinements. When phasing done, it created 8 chains for dimer protein (~750 
aa's per unit). So I am using NCS for refinement in each cycle. My question is 
that how to choose the best chains to refine in coot before I do the SSM 
superpose, Merge and then run the refinement. I am also trying to try 
auto-build if R-values don't come down. Any suggestions or education is 
welcomed.
Thanks and cheers.

Chetan Arya
Instem, Bangalore
India 560065



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[ccp4bb] Selecting best chain for NCS

[Chetan A]

Hello All,
I am trying to refine some protein structure and right now my structure's
R-free is not coming down from 37% even the R-work is lowering in each
round of refinements. When phasing done, it created 8 chains for dimer
protein (~750 aa's per unit). So I am using NCS for refinement in each
cycle. My question is that how to choose the best chains to refine in coot
before I do the SSM superpose, Merge and then run the refinement. I am also
trying to try auto-build if R-values don't come down. Any suggestions or
education is welcomed.
Thanks and cheers.

Chetan Arya
Instem, Bangalore
India 560065



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[ccp4bb] crystallographer position at Brown University

[Alexandra Deaconescu]

Please see below an ad for a position in my lab.

*Structural Biologist Position at*

*at Brown University, USA*

The Deaconescu Lab at Brown University has one opening for a structural 
biologist. The laboratory's interests lie primarily in stress responses, 
with particular emphasis on responses to DNA damage and the 
mechanochemistry of DNA-based motors. We utilize a combination of 
biochemical, biophysical and structural techniques. (e.g. X-ray 
crystallography, small-angle X-ray scattering, transmission electron 
microscopy). For examples of work, please see Vemu et al. /Science 
/(2018), Le TT et al. /Cell/ (2018), Deaconescu et al. /Photochemistry 
and Photobiology /(2017), Kutter et al. /JMB/ (2016), Szyk et al, /Cell/ 
(2014), Deaconescu et al., /PNAS/ (2012), Szyk et al., /NSMB/ (2012) and 
Deaconescu et al., /TIBS/ (2013).


A successful candidate should have _an established track-record of 
publications in peer-reviewed journals_. Solid experience with protein 
biochemistry (including their purification from E.coli/yeast expression, 
functional characterization and assay development) is desirable*. 
P**_rior knowledge of crystallography and/or single-particle electron 
microscopy is essential_*. Crystals/data at various stages of the 
structure determination process are available for immediate work. 
Responsibilities include crystal freezing, data collection and 
processing, obtaining and interpreting maps (X-ray or cryo-EM), model 
building, refinement and deposition of structures.  Additionally the 
candidate will participate in the teaching and training of other lab 
members. Overall responsibilities and compensation will depend on 
qualification and performance.


Must be highly motivated and work independently as well as in a team. 
Excellent spoken and written English are required. New Ph.D. graduates 
are encouraged to apply.


*Interested candidates should send a CV, one page research experience 
summary and contact information for three references to 
**_alexandra_deacone...@brown.edu 
_**.*Salary and starting date are 
negotiable.Brown University, an Ivy League school, is located less than 
one hour away by train from Boston.Lab webpage: https://deaconesculab.com


--
Alexandra Deaconescu, B.E., Ph.D.
Assistant Professor
Brown University

Office: (401) 863-3215
Wet Lab: (401) 863-6729
Computational Lab: (401) 863-7031

For Mail:
Laboratories of Molecular Medicine
70 Ship St. GE-4
Providence, RI 02903

For Courier:
Laboratories of Molecular Medicine
Brown University
70 Ship St., Chestnut St. Loading Dock
Providence, RI 02903

Website: www.deaconesculab.com

Admin
Ms. Christina Fournier
Email: christina_fournier[at]brown.edu
Mailing Address:
Box G-E, Brown University,
Providence, RI 02912-G
Telephone: 401-863-2782

Confidentiality Notice:
This e-mail message, including any attachments, is for the sole use of the 
intended recipient(s) and may contain confidential, proprietary and privileged 
information. Any unauthorized review, use, disclosure or distribution is 
prohibited. If you are not the intended recipient, please contact the sender 
immediately and destroy or permanently delete all copies of the original 
message.




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[ccp4bb] Reminder about RapiData at SSRL 2019 - less than a month left to apply!

[Smith, Clyde]

Hi all,

Just a reminder that the applications for the RapiData 2019 @ SSRL workshop 
close at the end of this month, December 31 2018. The workshop will be held 
from May 5-10 2019 on the SLAC campus.

The course will comprise hands-on experiments at the SSRL beamlines, software 
tutorials, and lectures on the following topics: Specimen preparation, Data 
collection strategies, X-ray light sources, X-ray detectors, Data reduction, 
Structure solution by MAD, SAD and Molecular Replacement, Complementary methods 
(spectroscopy and small angle scattering).

Please visit http://smb.slac.stanford.edu/news/rapidata/rapidata-2019/ and use 
the links on the "registration" page to apply for the course. Successful 
applicants will be notified early in January 2019 and invited to register. A 
limited amount of travel support funding may be available.

We look forward to seeing you all out in sunny California in May 2019!

Silvia Russi, Clyde Smith and Jeney Wierman (Organizers)
sru...@slac.stanford.edu
jwier...@slac.stanford.edu
csm...@slac.stanford.edu



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[ccp4bb] post: Single Particle Analysis Scientific Workflows App

[Vos, Matthijn R.]

Dear moderator, could you please post the following text:

Dear colleagues:

In addition to the Getting Started in Cryo-EM video series, Thermofisher 
Scientific has now released the Scientific Workflows iOS App (Android will be 
available in January). This App includes the videos split up in a step-by-step 
guide. It contains a full text SPA workflow (more workflows will be added) with 
extensive search functionality. The workflow steps contain links to related 
parts of the videos. Also the full em-learning.com content is available via the 
App.

This Scientific Workflows iOS App can be downloaded here:
https://itunes.apple.com/us/app/scientific-workflows/id1182342654?mt=8

Click on "Or start the lite version" link at the login screen to enjoy all free 
features.

Enjoy!

Benice van Gerven, Thijs Bressers and Matthijn Vos


Dr. Matthijn R. Vos
Sr. Staff Client Services Project Manager
Materials & Structural Analysis

Thermo Fisher Scientific
Achtseweg Noord 5 | 5651 GG Eindhoven | The Netherlands
Phone +31 6 23515172
matthijn@thermofisher.com




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Re: [ccp4bb] 2 Scientists (f/m/diverse) at Beamline P11, PETRA III

[Heinrich Zimmermann]

2 Scientists (f/m/diverse) at Beamline P11, PETRA III

We are seeking two highly motivated scientists (f/m/diverse) to enhance
our macromolecular crystallography research team at this state-of-the-art
beamline at DESY in Hamburg, Germany.

DESY is one of the world’s leading research centres for photon science,
particle and astroparticle physics as well as accelerator physics. More
than 2400 employees work at our two locations Hamburg and Zeuthen in
science, technology and administration.

Looking back on a long tradition in research with synchrotron radiation,
DESY is one of the leading centres in the field of photon science
worldwide. With the storage ring PETRA III and the Free-Electron-Laser
FLASH, DESY offers a unique combination of photon sources to the
scientific community. PETRA III, one of the most brilliant hard X-ray
facilities worldwide, currently provides 20 undulator beamlines for
experiments utilizing the extreme source brilliance. The 'Bioimaging and
Diffraction Beamline P11' provides extremely high flux denisities allowing
for ultra-fast 3D structure determination of biological samples.

What we offer:

·   Develop and pursue own independent research projects in the field
of macromolecular and serial crystallography

·   Commissioning of new instrumentation and implementation of new
techniques and software applications at the beamline

·   Work in an interdisciplinary team in very close collaboration with
the user community

·   User support at P11

What we're looking for:

·   PhD in biochemistry, chemistry or a related field

·   Strong background in X-ray crystallography and protein structure
determination using synchrotron radiation and/or free electron lasers are
required

·   Good experimental skills and strong interest in instrumentation
development are beneficial

·   Programming skills in Python or C++ would be an asset

For further information please contact Dr. Anja Burkhardt 040-8998-1775,
 anja.burkha...@desy.de.

The position is limited to 2 years.

We are looking forward to your application (including CV, research
experience, and two names and contact information for references) via our
application system:  
www.desy.de/onlineapplication

Deutsches Elektronen-Synchrotron DESY

Code: FSPO020/2018

Notkestraße 85 | 22607 Hamburg Germany

Phone: +49 40 8998-3392

http://www.desy.de/career

Deadline for applications: 2018/12/11

With best regards

Heinrich Zimmermann

--

Heinrich Zimmermann

Personnel Officer HR Recruitment

Human Resources (V2)

Deutsches Elektronen-Synchrotron DESY

A Research Center of the Helmholtz Association

Notkestr. 85, 22607 Hamburg

phone: 040-8998-1589

fax: 040-8998-3282

email: heinrich.zimmerm...@desy.de

web: http://www.desy.de

for guests: building 07 room 502



WE ARE RECRUITING!

Become a Part of us. You can find our current job openings right here:
www.desy.de/jobs

We are looking forward to your application!




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[ccp4bb] Post doctoral position in hit discovery for the TPP riboswitch (Bergen, Norway)

[Ruth Brenk]

Hi,

I have an open position in my group at the University of Bergen (Norway) 
for hit discovery for the TPP riboswitch.



I am looking for somebody with experience in at least one of the 
following areas:


-    In vitro transcription of RNA
-    HTS assay development
-    X-ray crystallography of macromolecules
-    development of small molecule binding assays using SPR

Additional experience in any of the following fields will be an advantage:
-   structure-based ligand design using computational methods
-   diffraction data collection at synchrotron beamlines
-   work experience in a multidisciplinary team including medicinal 
chemists and biologists


More information can be found here: 
https://www.jobbnorge.no/ledige-stillinger/stilling/161277/postdoctoral-fellow-3-years-for-hit-discovery-for-riboswitches



You are welcome to contact me for more information but the application 
has to be send via jobbnorge.no.



Regards

Ruth

--
Prof. Dr. Ruth Brenk
University of Bergen
Department of Biomedicine

ruth.br...@uib.no
+47 55586070

Visitor adress:  Mail address:
Jonas Lies vei 91Postboks 7804
5020 Bergen  5020 Bergen
Norway   Norway

 




 





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[ccp4bb] Expert in Computational Structural Biology, Friedrich Miescher Institute, Basel, Switzerlnd

[Chao, Jeffrey]

Dear Colleagues-

The Friedrich Miescher Institute for Biomedical Research (FMI) seeks an expert 
in Computational Structural Biology with a strong background in 
state-of-the-art approaches to structure solving, including low-resolution 
X-ray structures, model building and refinement.  The FMI is a world-leading 
research institute located in Basel, Switzerland, focusing on fundamental 
questions of medical relevance.  Research groups at the FMI use both X-ray 
crystallography and single-particle cryogenic electron microscopy for 
determining the structures of macromolecular complexes.

Candidates should have a PhD degree in structural biology or a related field.  
Responsibilities include obtaining and interpreting maps (X-ray or cryo-EM), 
model building, refinement and deposition of structures.  Additionally the 
candidate will participate in the teaching and training of PhD students and 
postdocs.  Overall responsibilities and compensation will depend on 
qualification and performance.

Closing date for applications is January 10, 2018

For further details and information on how to apply:

https://www.fmi.ch/Careers/JobDetails.html?jobID=246

Jeffrey Chao
Group Leader
Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
CH - 4058 Basel
Phone: +41 79 536 61 03
jeffrey.c...@fmi.ch







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Re: [ccp4bb] photograph of Enraf-Nonius FAST detector

[Harry Powell]

Hi Gerard 

That's a lovely picture - many thanks. I haven't seen Thierry for a long time - 
how is he? Did I miss him in Oviedo?

On 3 Dec 2018, at 09:05, Gerard Bricogne wrote:

> Dear Harry,
> 
> Your last sentence below made me think that you might well be
> interested in this detector, the Mark II multiwire chamber that was
> built by Georges Charpak at CERN for Roger Fourme and Richard Kahn at
> LURE. It was this detector that enticed me to go and work at LURE, and
> it was in order to create appropriate software for it that I organised
> and ran the EEC Area Detector Software Workshop (1986-1989) that is
> still quoted nowadays as the inspiration for the DIALS project.
> 
> It was on this detector that Wayne Hendrickson came to collect a
> MAD dataset on a Holmium derivative (I think) of Bill Weiss's mannose
> binding protein, using the re-engineered MADNESS software written
> during the Workshop (it was fashionable for everything to be called
> MAD in those days ...) . The monochromator was not very well behaved
> and produced a continuous drift in wavelength that had to be tracked
> as part of the subsequent phase calculations, but the detector itself
> performed superbly. Unfortunately it was limited by its technology to
> an overall counting rate of about 500k counts/second. 
> 
> I hope this will enhance your collection of obsolete detectors.
> This one was a unique copy. I want to thank Thierry Prangé for sending
> me this picture during the summer.
> 
> 
> With best wishes,
> 
>  Gerard.
> 
> --
> On Tue, Nov 27, 2018 at 12:48:07PM +, Harry Powell wrote:
>> Hi Elspeth
>> 
>> That's brilliant - no, it's not too late by any means. Photos of other 
>> obsolete detectors are also welcome!
>> 
>> 
>> On 27 Nov 2018, at 12:40, Elspeth Garman wrote:
>> 
>>> I have one of the LMB Cambridge one. 
>>> Can dig it out for you but not till Monday. Is that too late?
>>> Elspeth 
>>> 
>>> Sent from my iPhone
>>> 
>>> On 27 Nov 2018, at 12:35, Harry Powell 
>>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>>> 
 Hi
 
 I was wondering if anyone out there has a decent-quality photograph of an 
 Enraf-Nonius FAST detector that I could use? I believe that one was 
 installed at SRS Daresbury in 1983...
 
 Harry
 --
 Dr Harry Powell
 
>> 
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
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> 
> -- 
> 
> ===
> * *
> * Gerard Bricogne g...@globalphasing.com  *
> * *
> * Global Phasing Ltd. *
> * Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
> * Cambridge CB3 0AX, UK   Fax: +44-(0)1223-366889 *
> * *
> ===
> 
> 
> 
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Re: [ccp4bb] photograph of Enraf-Nonius FAST detector

[Harry Powell]

Hi Ben

Thanks for this - if what you're seeing is what I get when I use that URL it's 
not quite as useful as I would have hoped! I did ask the Science Museum if they 
had any photos of kit that is not in their current photographic collection and 
they offered to take the photos for , so I declined. I might pop down to 
South Ken and see what's on public display that I can get a picture of that is 
(perhaps, I'd have to check carefully) unencumbered by their various 
copyrights...

Harry

On 2 Dec 2018, at 21:29, benjamin bax wrote:

> 
> Hi Harry,
>   I think some old stuff from Birkbeck crystallography teaching labs. went to 
> science museum.
> 
> However, picture of 
> Enraf-Nonius Weissenberg X-ray camera, model Y809, (X-ray diffraction camera) 
> - from 1968 - does not look quite like what I remember.
> 
> https://collection.sciencemuseum.org.uk/search?q=Enraf-Nonius%20Weissenberg%20X-ray%20camera%2C%20model%20Y809%2C%20(X-ray%20diffraction%20camera)
> 
> Ben
> 
> 
> 
> On 27 Nov 2018, at 12:48, Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi Elspeth
> 
> That's brilliant - no, it's not too late by any means. Photos of other 
> obsolete detectors are also welcome!
> 
> 
> On 27 Nov 2018, at 12:40, Elspeth Garman wrote:
> 
>> I have one of the LMB Cambridge one. 
>> Can dig it out for you but not till Monday. Is that too late?
>> Elspeth 
>> 
>> Sent from my iPhone
>> 
>> On 27 Nov 2018, at 12:35, Harry Powell 
>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>>> Hi
>>> 
>>> I was wondering if anyone out there has a decent-quality photograph of an 
>>> Enraf-Nonius FAST detector that I could use? I believe that one was 
>>> installed at SRS Daresbury in 1983...
>>> 
>>> Harry
>>> --
>>> Dr Harry Powell
>>> 
> 
> 
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> 




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