[ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

[Alex Lee]

Dear All,

Is there a tool or software which can give Ramachandran information of
individual residues in a plot?

I used Coot to check for Ramachandran plots, but it shows all the residues
in a coordinate I put in Coot, not individual one. I also use "residue
info" in coot, it tells Ramachandran "phi psi" angles of individual
residue, but it does not show it in a plot, only numbers.

Thanks ahead for any input.

Re: [ccp4bb] XDS plugin for efficient reading of HDF5 data

[Kay Diederichs]

Dear all,

unfortunately the very latest BUILT of the XDS package (which fixed a problem 
in XDSCONV) introduced a last-minute bug in the routine that uses the "Neggia" 
plugin. This is documented, together with two workarounds, in the 
Troubleshooting section of the Eiger article in XDSwiki : 
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Eiger#Troubleshooting
 .

The easiest workaround is to just use the 20161205 BUILT of the XDS package 
(replacing the old XDSCONV with the one from the latest BUILT).
 
Sorry about this!

Kay


On Thu, 23 Mar 2017 10:56:54 +0100, Andreas Förster 
 wrote:

>Dear all,
>
>DECTRIS is proud to announce the release of an HDF5 read plugin to take
>advantage of the recently added XDS plugin support (thanks to Wolfgang
>Kabsch and Kay Diederichs) and accelerate the reading of HDF5 files.
>
>EIGER detectors produce data in the large-data format HDF5. Despite
>substantial advantages (few files to handle, excellent compression), HDF5
>data pose some difficulties.  While DIALS and HKL-2000 process HDF5 data
>natively, they are limited in their performance by the lack of parallel
>reading of the HDF library.  Processing of HDF5 data by XDS has thus far
>relied on extraction of temporary CBF images, which adds to the processing
>time.
>
>Neggia, our read plugin for XDS, presents HDF5 data to XDS in a fully
>parallelized way, directly and without interconversion.  Processing of HDF5
>data is now as fast as processing of CBFs.  Refer to the plugin with LIB=
>/path/to/plugin.so in XDS.INP.  The parameter DETECTOR= EIGER should remain.
>
>You can download the plugin from www.dectris.com/neggia.html (registration
>required).  To run it you need a reasonably recent OSX or linux system with
>gcc 4.8 or higher.  We have tested macOS Sierra, CentOS 6, CentOS 7, Mint
>17.3.  Alternatively, you can compile the plugin from the source available
>at https://github.com/dectris/neggia.
>
>The plugin was written to work with recent EIGER data and has been tested
>in house and at a few adventurous beamlines.  If you encounter issues,
>please let me now.  Your problem reports will help make the plugin better,
>to the benefit of the entire community.
>
>All best and happy data processing
>
>
>Andreas
>
>
>
>-- 
>
>Andreas Förster, Ph.D.
>MX Application Scientist, Scientific Sales
>Phone: +41 56 500 2100 | Direct: +41 56 500 2176 | Email:
>andreas.foers...@dectris.com
>DECTRIS Ltd. | Taefernweg 1 | 5405 Baden-Daettwil | Switzerland |
>www.dectris.com
>
>[image: LinkedIn] 
> [image: facebook]
>
>
>
>
>
>
>
>Confidentiality Note: This message is intended only for the use of the
>named
>recipient(s) and may contain confidential and/or privileged information. If
>you
>are not the intended recipient, please contact the sender and delete the
>message.
>Any unauthorized use of the information contained in this message is
>prohibited.
>

[ccp4bb] Major upgrade of the STARANISO server

[Gerard Bricogne]

Dear all,

 The STARANISO server has now successfully processed over 1000
user-submitted datasets since it was launched in January last year.

 We are pleased to announce a major upgrade to this server:

* it now supports submissions of unscaled and unmerged intensity data
  (as well as the already available input mode for merged intensity
  data) and performs an analysis of anisotropy as part of the scaling
  and merging process;

* the documentation on the server concerning anisotropy in general and
  its treatment in STARANISO has been greatly expanded and includes a
  glossary for all the terminology used;

* similarly, the logfile now includes careful specifications for the
  various types of statistics (some of them, unfamiliar) it presents.

 We are still working hard on producing a template (with examples)
for an "anisotropy aware" Table 1, as well as an FAQ, but we thought
that now would be a good time to solicit a first round of feedback
from the user community: please connect to

 http://staraniso.globalphasing.org/cgi-bin/staraniso.cgi


 Ian Tickle and the Global Phasing developers.

[ccp4bb] Joint PhD Studentship - University of Sussex and Diamond Light Source.

[Erika Mancini]

Diamond Light Source – University of Sussex Joint 4 year PhD Studentship

Structural and Mechanistic Insights into the Mechanism of Chromatin Remodelling 
and DNA Damage Repair by CHD ATPases


Applications are invited for a 4 year PhD Studentship based jointly at the 
University of Sussex and Diamond Light Source.


Supervisors:
Dr Erika Mancini, Reader in Biomedical Structural Biology School of Life 
Sciences, University of Sussex
Dr Ralf Flaig, Senior Beamline Scientist, Diamond Light Source


Project Outline
Chromatin is a dynamic structure that shapes the spatial organization of 
genetic information within the nucleus to satisfy the ever-changing demands of 
the cellular environment. The architecture of chromatin is controlled by a 
bewildering multitude of regulatory factors amongst which are ATP-dependent 
chromatin remodellers. Using energy from ATP hydrolysis these enzymes modify 
the contact points between DNA and histones, thereby affecting chromatin at 
every level, from the spacing of nucleosomes to its overall superstructure.
The PhD project aims to provide a structural and functional description of the 
mechanism of remodelling of the CHD Chromatin remodelling ATPase family. 
Techniques employed will range from cellular biology, to understand the role of 
these proteins in the DNA damage repair pathway, through to biochemistry, 
biophysics and integrative structural biology (X-ray crystallography, SAXS, 
cryo-EM). The student will benefit from access to the most advanced methodology 
currently available to collect structural data at a Synchrotron source and to 
an expert environment to progress the research project efficiently. 
Furthermore, the nature of the samples will require the state-of-the-art 
facilities available at Diamond including eBIC and BioSAXS and specialised MX 
beamlines.


Workplace
The Sussex School of Life Sciences, soon to be relocated into a new 
state-of-the-art landmark building, provides a multidisciplinary, stimulating 
and supportive environment for post-graduate students. The University of Sussex 
is just nine minutes by train from Brighton, one of the UK’s most vibrant 
cities. The city is famous for its beautiful seafront, unique shops and 
markets, and thriving music and art scenes. Diamond Light Source is the UK’s 
national synchrotron and a leading scientific facility of its type in the 
world. Located on the Harwell Science and Innovation Campus in South 
Oxfordshire, it hosts research facilities supporting cutting edge research in 
all fields of science. Structural biology is a key research area and is 
supported by several MX and life science related beamlines and world leading 
facilities on the campus.


Eligibility and Funding
Ideal candidates will have a strong background in molecular biology and 
structural biology and a clear understanding of interest in the processes of 
gene expression and transcription regulation. Eligible candidates will have 
recently received an MSc and/or a First or high 2:1 BSc in a relevant subject. 
Due to restrictions on the funding this studentship is open to UK/EEU nationals 
students only. The studentship provides UK/EU tuition fees, a stipend (£16,300 
per year) and funds towards travel between sites and conference attendance.


Application and Deadlines:
Submit your application using the online application system at 
http://www.sussex.ac.uk/study/pg/applying/. Please make sure you include the 
project title and your statement of interest on the application form. On the 
application system use Programme of Study – PhD BIOCHEMISTRY. Deadline: 22nd 
April 2017. Interviews will take place by Skype or in person shortly 
thereafter. Informal enquiries may be addressed to: Dr Erika Mancini 
(erika.manc...@sussex.ac.uk) or Dr Ralf 
Flaig (ralf.fl...@diamond.ac.uk). For 
application queries, please contact Anna Izykowska: 
a.izykow...@sussex.ac.uk

[ccp4bb] Further information on the HDF5 read plugin for XDS

[Andreas Förster]

Dear all,


after the announcement of the plugin a few minutes ago, I would like to
give some more detail for those who are interested.


1) The point of the plugin architecture is the logical separation between
data and program.  With plugins written for input data, program developers
can focus on improving their algorithms instead of dealing with data
formats.  There is no reason the ideas behind the plugin couldn't be used
by HKL-2000, Mosflm, DIALS or any other program that processes EIGER images
from HDF5 data.


2) The source code of Neggia has been released under MIT license (open
source) at https://github.com/dectris/neggia.  Feel free to identify
shortcomings and improve the code.


3) Neggia doesn't rely on the official HDF5 library.  As it makes
assumptions about the inner structure of HDF5 files, modifications might
throw it off.  Data written with the EIGER Filewriter can be read.  HDF5
data written from the Stream or where the master file has been modified
after data collection might pose problems.  We are working with beamlines
to make sure all EIGER data can be read by Neggia.  If you encounter
problems, please let me (and your beamline) know.  You can still process
the data with whatever approach you used before adopting the library.


4) The plugin mechanism of XDS is generic.  Anyone can write a plugin to
take advantage of it.  This might be useful to manufacturers of future
detectors with unsupported data formats.  The plugin communicates with XDS
through four function calls:
- subroutine generic_get_header (nx, ny, nbyte, qx, qy, number_of_frames,
info_array, error_flag)

- subroutine generic_open (library, template_name, info_array, error_flag)

- subroutine generic_get_data (frame_number, nx, ny, data_array,
info_array, error_flag)

- subroutine generic_close (error_flag)

If you think you can write more efficient read routines for already
supported formats, please contact Kay Diederichs.


All best.



Andreas



-- 

Andreas Förster, Ph.D.
MX Application Scientist, Scientific Sales
Phone: +41 56 500 2100 | Direct: +41 56 500 2176 | Email:
andreas.foers...@dectris.com
DECTRIS Ltd. | Taefernweg 1 | 5405 Baden-Daettwil | Switzerland |
www.dectris.com

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you
are not the intended recipient, please contact the sender and delete the
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[ccp4bb] XDS plugin for efficient reading of HDF5 data

[Andreas Förster]

Dear all,

DECTRIS is proud to announce the release of an HDF5 read plugin to take
advantage of the recently added XDS plugin support (thanks to Wolfgang
Kabsch and Kay Diederichs) and accelerate the reading of HDF5 files.

EIGER detectors produce data in the large-data format HDF5. Despite
substantial advantages (few files to handle, excellent compression), HDF5
data pose some difficulties.  While DIALS and HKL-2000 process HDF5 data
natively, they are limited in their performance by the lack of parallel
reading of the HDF library.  Processing of HDF5 data by XDS has thus far
relied on extraction of temporary CBF images, which adds to the processing
time.

Neggia, our read plugin for XDS, presents HDF5 data to XDS in a fully
parallelized way, directly and without interconversion.  Processing of HDF5
data is now as fast as processing of CBFs.  Refer to the plugin with LIB=
/path/to/plugin.so in XDS.INP.  The parameter DETECTOR= EIGER should remain.

You can download the plugin from www.dectris.com/neggia.html (registration
required).  To run it you need a reasonably recent OSX or linux system with
gcc 4.8 or higher.  We have tested macOS Sierra, CentOS 6, CentOS 7, Mint
17.3.  Alternatively, you can compile the plugin from the source available
at https://github.com/dectris/neggia.

The plugin was written to work with recent EIGER data and has been tested
in house and at a few adventurous beamlines.  If you encounter issues,
please let me now.  Your problem reports will help make the plugin better,
to the benefit of the entire community.

All best and happy data processing


Andreas



-- 

Andreas Förster, Ph.D.
MX Application Scientist, Scientific Sales
Phone: +41 56 500 2100 | Direct: +41 56 500 2176 | Email:
andreas.foers...@dectris.com
DECTRIS Ltd. | Taefernweg 1 | 5405 Baden-Daettwil | Switzerland |
www.dectris.com

[image: LinkedIn] 
 [image: facebook]







Confidentiality Note: This message is intended only for the use of the
named
recipient(s) and may contain confidential and/or privileged information. If
you
are not the intended recipient, please contact the sender and delete the
message.
Any unauthorized use of the information contained in this message is
prohibited.