[ccp4bb] Opportunities to work with EMDB/EMPIAR at EMBL-EBI, Hinxton UK

[Ardan Patwardhan]

Dear all

We have two open positions to work with EMDB/EMPIAR. More details can be found 
here: 

EM Data Content Specialist and Scientific Programmer:
https://www.embl.de/jobs/searchjobs/index.php?ref=EBI_01006 



EM Validation Scientific Programmer:
https://www.embl.de/jobs/searchjobs/index.php?ref=EBI_01011 


Best wishes

Ardan Patwardhan
Team Leader - Cellular Structure & 3D Bioimaging
EMDB & EMPIAR
European Bioinformatics Institute (EMBL-EBI) European Molecular Biology 
Laboratory
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
Tel: +44 1223 492649

Re: [ccp4bb] Fast searching of articles related to your PubMed indexed paper

[Smith Liu]

can you updated the server so that the most recent articles can be found?



发自网易邮箱大师


在2017年07月25日 11:49，Yaoqi Zhou 写道：
Fast searching of articles related to your PubMed indexed paper  

Are you spending too much time searching the literature to prepare your grant 
proposals, manuscripts and keeping track of research happening in your field? 
We have built a literature-based search engine 
(http://pubmed.ict.griffith.edu.au/) which is powered by a combination of 
state-of-the-art methods to locate relevant articles to your published 
PubMed-indexed papers within a few seconds.

While providing you the ability to locate relevant articles, we are seeking 
your feedback regarding the performance of these algorithms. By annotating 
recommended articles as relevant, somewhat relevant, or irrelevant, you are 
participating in a community-wide effort of establishing a gold-standard 
benchmark for relevant literature search.

The accuracy of this benchmark is ensured by your domain knowledge and 
experience as your judgements will be based in the context of your own article. 
With your expertise, the entire process will take only a few minutes to 
complete (1 paper, 6 recommendations). Upon completion, this community-wide 
dataset will be available to freely download and redistribute, encouraging 
development of next-generation literature searching and retrieval 
methodologies, something we all desperately need.

Due to current data availability, this relevant-paper search is limited to 
papers indexed by PubMed between January 1, 2007 to December 31, 2016 (the end 
of last year). Click http://pubmed.ict.griffith.edu.au/ to start. As this is a 
product in development, any constructive comments and suggestions will be truly 
appreciated.

If you like this idea of community-wide benchmark for literature 
recommendation, please forward this email to your colleagues in the scientific 
community.

Initial feedbacks to our server. “The process was certainly fast!”, “Although 
the articles found in the search were not necessarily exactly relevant, many 
are articles that I don't think I would have come across easily with a 
traditional search”, “Very nice work. I think there can be a longer list” 
(limited to 30 currently).

Thank you!

Yaoqi

Professor Yaoqi Zhou | Research Leader
Institute for Glycomics
Griffith University | Gold Coast campus | QLD 4222 | Institute for Glycomics 
(G24) Room 2.10
T +61 7 5552 8228 | F +61 7 5552 9040 | email yaoqi.z...@griffith.edu.au 

http://sparks-lab.org (Group webpage)

http://griffith.edu.au/institute-glycomics (Institute Webpage)

On 25 Jul 2017, at 9:01 AM, CCP4BB automatic digest system 
 wrote:


There are 14 messages totaling 9878 lines in this issue.

Topics of the day:

 1. Buccaneer places residues in different asymmetric units (3)
 2. Primer design (7)
 3. PhD position at University of Oslo
 4. Postdoctoral position at Boston Children’s Hospital
 5. About weighting factor settings in new ccp4i2 (2)

--

Date:Mon, 24 Jul 2017 16:56:51 +0800
From:Lingxiao Zeng 
Subject: Buccaneer places residues in different asymmetric units

Dear All,

I tried to use buccaneer to build a model. The starting model is a partial 
model, after model building the Rwork and Rfree are reasonable but buccaneer 
places residues in different asymmetric units and the model looks really weird.

Is there any way to build the model into the same ASU or put different parts 
together after model building? Thanks!



Best,

Alice

--
Lingxiao Zeng
PhD candidate
School of Biomedical Sciences
The University of Hong Kong

--

Date:Mon, 24 Jul 2017 10:35:17 +0100
From:Jon Agirre 
Subject: Re: Buccaneer places residues in different asymmetric units

Dear Alice,

there's an option in both ccp4i and ccp4i2 interfaces that lets you tell
Buccaneer that you want to build the new model in the same place as the
partial model supplied - see my screenshots for reference. It might not be
on by default and perhaps it should be.

Please be aware that most newer developments and improvements will be put
on the ccp4i2 interface to Buccaneer - it would be helpful if you could
have a go and let us know what you think!

Hope this helps,

Jon

On 24 July 2017 at 09:56, Lingxiao Zeng  wrote:

Dear All,


I tried to use buccaneer to build a model. The starting model is a partial
model, after model building the Rwork and Rfree are reasonable but
buccaneer places residues in different asymmetric units and the model looks
really weird.


Is there any way to build the model into the same ASU or put different
parts together after model building? Thanks!




Best,

Alice

--
Lingxiao Zeng
PhD candidate
School of Biomedical Sciences
The University of Hong Kong




--
Dr Jon Agirre
York Structural Biology Laboratory / Department of 

[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline September 01, 2017

[Manfred S. Weiss]

Next MX-proposal application deadline: September 01, 2017 is approaching
http://www.helmholtz-berlin.de/user/beamtime/proposals/index_en.html

Hereby we would like to invite the submission of new proposals for
MX-beamtime at the HZB-MX beamlines for the next beam time period
(02/2018-08/2018).

In order to apply for beamtime, please register at the HZB on-line
access tool "GATE" (https://www.helmholtz-berlin.de/pubbin/hzbgate)
and submit a new beam time application proposal.

What's new: Helical data collection will be possible on BL14.1 !!!

HZB provides MX-beamtime at the three MX-beamlines BL14.1, BL14.2
and BL14.3. The three beamlines are equipped with state-of-the-art
instrumentation and are currently the most productive MX-stations
in Germany with over 500 PDB depositions in 2016 alone. Beamtime
is granted based on the reviewed proposals and on reports from
previous research activities. Please make sure to include them if
available.

Experimental setup:

BL14.1:
- Photon flux: 1.4x10¹¹ Phot/sx100mAx0.05%BW at sample position
 (0.1-1 sec exposure time per frame)
- User defined beam shaping from 50µm-100µm diameter possible
- Pilatus 6M detector, 141mm-680mm max. distance from the sample
- Microdiffractometer (MD2) with Mini-kappa goniometer MK3
- Automatic sample changer (CATS), 90 sample storage capacity
 (SPINE-Pin & EMBL sample magazine compatibility)
- 32-core XEON-CPU server, with 10Gb uplink to Pilatus 6M
- Data collection control via MXCuBE
- EDNA
- Common MX-software installed including XDS, iMOSFLM, CCP4,
 Phenix, SHELXC-E, etc.
- Automated data processing with XDSAPP2.0
- Remotely controlled cryo-shutter for crystal annealing
- Pressure chamber for noble gas derivatization (Xe, Kr
 available upon request)
- AMPTEK-XRF detector and XFEPLOT software available

We are also offering the hard- and software environment for
carrying out:
- UV-RIP experiments at BL14.1. For further information, please visit:

http://www.helmholtz-berlin.de/forschung/funkma/soft-matter/forschung/bessy-mx/ancillary-facilities/uvrip_en.html

BL14.2:
- Photon flux: 1.9x10¹¹ Phot/sx100mAx0.05%BW at sample position
 (0.1-1 sec exposure time per frame)
- Pilatus 3S-2M detector with 1000 micron Si sensor thickness,
 55mm-600mm distance from the sample
- Nanodiffractometer (DESY P11 design) and on-axis sample microscope
- User defined beam shaping from 30µm-150µm diameter possible
- GROB sample changer for SPINE and UNIPUCK support
- 60-core XEON-CPU server, with fibre channel SAN up-link data
 processing environment
- Common MX-software installed including XDS, iMOSFLM, CCP4, Phenix,
 SHELXC-E, etc.
- Automated data processing with XDSAPP2.0
- Amptek XRF detector
- Pressure chamber for noble gas derivatization (Xe, Kr available
 upon request)
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom,
 8 Mpixel CCD-camera
- UV-Microsprectrophotometer offline setup available
- AMPTEK-XRF detector and XFEPLOT software available

BL14.3:
- Photon flux: 4x10exp10 Phot/sx100mAx0.05%BW at sample position
 (3-20 sec exposure time per frame)
- Rayonix MX-225 X-ray detector, 45mm-380mm distance from the
 sample, 30 deg 2-Theta possible
- MARdtb goniometer
- 60-core XEON-CPU server, with fibre channel SAN up-link data
 processing environment
- EDNA installed and available
- Common MX software installed including XDS, iMOSFLM, CCP4, Phenix,
 SHELXC-E, etc.
- Automated data processing using XDSAPP2.0
- Remotely controlled cryo-shutter for crystal annealing
- HC1c dehydration device installed (please specify HC1-beamtime
 in your proposal if needed)
- Pressure chamber for noble gas derivatization (Xe, Kr available
 upon request)
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom,
 8 Mpixel CCD-camera

S1-biolab facilities (separate registration required):
- Protein production and purification
- Nanoliter 96 well crystallization plate formulation and storage at
 5 °C and 20 °C
- Biophysical characterization with real time PCR (thermofluor assay)

The HZB-MX group is also providing expert assistance as well as
access to a library of fragments for carrying out crystallographic
fragment-screening experiments. For more information please read:
http://www.helmholtz-berlin.de/forschung/oe/em/soft-matter/forschung/bessy-mx/fragment-screening/index_en.html
or contact us at 
mswe...@helmholtz-berlin.de.

Please visit our web page 
www.helmholtz-berlin.de/bessy-mx to 
obtain
updated information about our experimental setup and other
requirements.

Manfred Weiss and the HZB-MX group

--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv.