[ccp4bb] Introducing Dials User Interface for CCP4

[luis.fuentes-mont...@diamond.ac.uk]

Dear ccp4bb,

I am happy to introduce you to the new Dials User Interface (DUI) for CCP4.

DUI is a graphical user interface that is designed to make data processing with 
DIALS more user-friendly and efficient. A key feature is a full history tree 
that keeps track of all steps of processing. Every position in the tree 
represents the execution of a DIALS command line with full record of the 
user-supplied parameters, and the results, which can be inspected with several 
visualisation tools. At any step, the user can either fork, proceed to the next 
command or navigate to another step without loss of information. This ability 
to keep track of different branches of data processing gives the user freedom 
to explore different hypotheses, such as the space group of the crystal.

DUI is intended to be intuitive and immediately useful across a wide range of 
user expertise. Beginners learning about the integration process with DIALS 
will benefit from the ease-of-use of the GUI and the visualisation tools. 
Experts retain full control of the underlying DIALS programs and can use the 
history tree to test different ideas quickly.

DUI does not have a launcher from ccp4i2 yet, but you can launch it by just 
typing dui from your terminal. I would recommend to cd to the directory with 
your images first. And of course have updated CCP4 to the latest version.

Enjoy!

Thanks,

Luis Fuentes-Montero (Luiso)


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Re: [ccp4bb] normal-coordinate structural decomposition (NSD) server?

[Sarah EJ Bowman]

Hi Mike,
 
Here is a link to a current NSD calculator for heme distortions from planarity 
available online from the Liptak Group in Vermont:
 
http://mliptak.w3.uvm.edu/nsd.html
 
This uses the method originally developed by Shelnutt.
 
Hope that helps!
Sarah

Re: [ccp4bb] normal-coordinate structural decomposition (NSD) server?

[Sarah Bowman]

Hi Mike,

Here is a link to a current NSD calculator for heme distortions from planarity 
available online from the Liptak Group in Vermont:

http://mliptak.w3.uvm.edu/nsd.html

This uses the method originally developed by Shelnutt.

Hope that helps!
Sarah


Sarah EJ Bowman, PhD

High-Throughput Crystallization Screening Center
Hauptman-Woodward Medical Research Institute
www.getacrystal.com

sbow...@hwi.buffalo.edu
716-898-8623

From: CCP4 bulletin board  on behalf of "Hough, Mike" 

Reply-To: "Hough, Mike" 
Date: Wednesday, May 2, 2018 at 11:14 AM
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: normal-coordinate structural decomposition (NSD) server?

Dear CCP4bbers,

I would like to analyse the out of plane distortions in a heme protein 
structure using the normal-coordinate structural decomposition (NSD) method. 
This would be a way to assess e.g. ruffling and saddling distortions. At one 
point this was available via a
web server at: http://jasheln.unm.edu/jasheln/content/nsd/nsd__welcome.htm


but this no longer seems to be active.

Is anyone aware if there is a new home for the server or alternatively a source 
of the program used?

Many thanks,

Mike

[ccp4bb] Post-doc position available at University of Texas Medical Branch (UTMB)

[Choi, Kyung]

Post-doc position at University of Texas Medical Branch (UTMB), TX, USA

Postdoctoral positions in structural biology are available in Dr. Kay Choi's 
laboratory at the University of Texas Medical Branch (UTMB) to participate in 
virus replication projects. We use a combination of X-ray crystallography, 
cryo-electron microscopy (cryo-EM), and biochemistry to investigate the 
structure and mechanism of viral macromolecular complexes. Experience in either 
X-ray crystallography, cryo-EM or biochemistry is required.  For more 
information please see ‘https://bmb.utmb.edu/faculty/choi.asp’

The X-ray crystallography resources at UTMB include two X-ray area detector 
systems, a Phoenix crystallization robot, a Minstrel crystal imaging robot, and 
an Alchemist liquid handling robot. The cryo-EM includes two JOEL 200 keV 
cryo-EM microscopes for high-resolution imaging work, an FEI vitrobot, and a 
BSL-3 room for viral and pathogen work.  For more information, please see 
‘https://scsb.utmb.edu/resources/default.asp’

Interested parties should send a cover letter, CV and a list of 2-3 references 
to Dr. Kay Choi via e-mail at kyc...@utmb.edu.

Kay

Kay Choi
Associate Professor
Department of Biochemistry and Molecular Biology
6.614C Basic Science phone 
: 409-747-1402
The University of Texas Medical Branch fax : 
409-747-1404
301 University Blvd.  
email : kay.c...@utmb.edu
Galveston, TX 77555-0647

Re: [ccp4bb] normal-coordinate structural decomposition (NSD) server?

[Hough, Mike]

Hi Sarah,

Fantastic, thank you!

Best wishes,

Mike


On 2 May 2018, at 16:20, Sarah Bowman 
> wrote:

Hi Mike,

Here is a link to a current NSD calculator for heme distortions from planarity 
available online from the Liptak Group in Vermont:

http://mliptak.w3.uvm.edu/nsd.html

This uses the method originally developed by Shelnutt.

Hope that helps!
Sarah


Sarah EJ Bowman, PhD

High-Throughput Crystallization Screening Center
Hauptman-Woodward Medical Research Institute
www.getacrystal.com

sbow...@hwi.buffalo.edu
716-898-8623

From: CCP4 bulletin board > 
on behalf of "Hough, Mike" >
Reply-To: "Hough, Mike" >
Date: Wednesday, May 2, 2018 at 11:14 AM
To: "CCP4BB@JISCMAIL.AC.UK" 
>
Subject: normal-coordinate structural decomposition (NSD) server?

Dear CCP4bbers,

I would like to analyse the out of plane distortions in a heme protein 
structure using the normal-coordinate structural decomposition (NSD) method. 
This would be a way to assess e.g. ruffling and saddling distortions. At one 
point this was available via a
web server at: http://jasheln.unm.edu/jasheln/content/nsd/nsd__welcome.htm


but this no longer seems to be active.

Is anyone aware if there is a new home for the server or alternatively a source 
of the program used?

Many thanks,

Mike

Re: [ccp4bb] normal-coordinate structural decomposition (NSD) server?

[Denis Rousseau]

John Shelnutt who wrote the program passed away so his web site no longer 
exists. I suggest you contact Bob Scheidt at Notre Dame Chemistry to get a copy 
of it.

Denis Rousseau

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Hough, Mike 
[maho...@essex.ac.uk]
Sent: Wednesday, May 02, 2018 11:13 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] normal-coordinate structural decomposition (NSD) server?

Dear CCP4bbers,

I would like to analyse the out of plane distortions in a heme protein 
structure using the normal-coordinate structural decomposition (NSD) method. 
This would be a way to assess e.g. ruffling and saddling distortions. At one 
point this was available via a
web server at: http://jasheln.unm.edu/jasheln/content/nsd/nsd__welcome.htm

but this no longer seems to be active.

Is anyone aware if there is a new home for the server or alternatively a source 
of the program used?

Many thanks,

Mike

[ccp4bb] normal-coordinate structural decomposition (NSD) server?

[Hough, Mike]

Dear CCP4bbers,

I would like to analyse the out of plane distortions in a heme protein 
structure using the normal-coordinate structural decomposition (NSD) method. 
This would be a way to assess e.g. ruffling and saddling distortions. At one 
point this was available via a
web server at: http://jasheln.unm.edu/jasheln/content/nsd/nsd__welcome.htm

but this no longer seems to be active.

Is anyone aware if there is a new home for the server or alternatively a source 
of the program used?

Many thanks,

Mike

[ccp4bb] Post-doctoral positions in the Netherlands Cancer Institute, Amsterdam

[Titia Sixma]

Two post-doctoral positions in the Netherlands Cancer Institute

Two post-doctoral positions are available in the Netherlands Cancer Institute 
in the group of Titia Sixma. We study mechanisms of enzyme regulation in DNA 
repair, using a combination of stuctural biology, biochemistry, biophysics and 
cellular assays. We are particularly focussed on processes of ubiquitin 
conjugation and DNA mismatch repair.

The institute is well set up for protein expression and characterisation 
(sharing equipment with the Protein Facility, an Instruct-ERIC and iNEXT 
participant), has an excellent computing infrastructure (hosting the NKI 
Research High Performance Computing Unit) and also regular, well-established 
access to testing and high resolution facilities for NMR, cryo-EM and 
synchrotrons. The labs and work discussions are shared with the groups of 
Tassos Perrakis and Robbie Joosten, who are interested in method development 
for structural biology (including the PDB-REDO project) as well as the group of 
Thijn Brummelkamp who is interested in developing and applying novel genetics 
approaches.

The Netherlands Cancer Institute is a center of excellence with a high standard 
of biological research and an interactive atmosphere, with shared group 
meetings and social events. Amsterdam is a liveable city, with its many 
cultural amenities within easy reach and within easy access to most European 
cities, through the closeby Schiphol airport (<30 minutes).

Currently we have vacancies for:

1)  An experienced crystallographer for a project focussing on 
crystallization of allosteric enzymes.

2)   A researcher with experience in cryo-EM for a project in DNA 
replication.
Appointments are for 3 years. Applicants should write an e-mail with 
motivation,  CV and names of three references to 
t.si...@nki.nl  before May 19th.

Titia Sixma
Division of Biochemistry
Netherlands Cancer Institute
Plesmanlaan 121
1066 CX Amsterdam