[ccp4bb] CCP4 7.0 update 040

[Charles Ballard]

Dear All, 

another update containing

* ccp4mg/mrbump 
 - improved sequence matching

* molrep
 - packing function improvement

* sfcheck
 - improved EM map handling

* ssm/mmdb
 - fix for bug in forced element name correction

* clipper
 - support for more non-standard spacegroup settings

* ctruncate
 - more stability in truncate procedure

available through ccp4i2, ccp4i and ccp4um on the command line

All the best

CCP4 core team

[ccp4bb] Fully automated intelligent data collection : MASSIF-1@ESRF

[Matthew Bowler]

Dear community,
the autonomous data collection beamline MASSIF-1 at the ESRF has now 
been running for 3 years and is highly successful. The service is 
available for all types of sample mount and crystals, from screening 
initial hits from crystallisation screens through to the collection of 
hundreds of data sets from well characterised systems.


Recent developments:

 * We now pay for dewar shipping to and from the ESRF for all peer
   reviewed academic experiments on MASSIF-1 (1 dewar per shift or 3
   dewars for 24 hours).  See http://www.esrf.eu/dewar for details.
 * Beam size is now adapted dynamically to the best diffraction volume
   in each crystal.
 * Multi position data collection and helical data collection now
   available.
 * You can now apply for completely automated high throughput fragment
   screening and data collection (in collaboration with the HTX lab at
   EMBL Grenoble) via iNEXT, see http://www.inext-eu.org/access/


Essential points:

1. Time is not scheduled but booked on-line when you need it via an 
online calendar in consultation with your BAG responsible - you can book 
regular slots or at short notice when you get crystals
2. If you are not part of a BAG you are welcome to apply for rapid 
access time here http://www.esrf.eu/MXnon-BAGproposal
3. No restriction on sample type - a rapid X-ray centring routine scans 
the full sample mount to locate and centre crystals (crystals <20um are 
regularly seen) If there is a crystal there MASSIF will find it!
4. Data collections can be tailored to each sample (resolution, space 
group, beam size, redundancy, SAD and more) via the ISPyB diffraction 
plan (http://www.esrf.fr/MXPressE)

5. Full results available in real time via ISPyB
6. No need to come to the beamline
7. Time deducted as a function of the number of samples processed

MASSIF-1 has a beam of 100 x 65 um (HxV), that can be defined by 
apertures from 50 um down to 10 um, and has a fixed energy of 12.8 keV 
with a flux of ~3 x 10e12 ph/s and a PILATUS3 2M detector.


The service has now been running for 3 years and is proving very 
popular, we have now processed over 30,000 crystals and many structures 
have been solved de novo by SAD. Details of the process and the beamline 
can be found in some recent publications:



Svensson, O., Monaco, S., Popov, A. N., Nurizzo, D. & Bowler, M. W. 
(2015). The fully automatic characterization and data collection from 
crystals of biological macromolecules, Acta Cryst. D71, 1757-1767, 
http://dx.doi.org/10.1107/S1399004715011918


Bowler, M.W., Nurizzo, D., et al. (2015). MASSIF-1: A beamline dedicated 
to the fully automatic characterisation and data collection from 
crystals of biological macromolecules, J. Synchrotron Rad. 22, 
1540-1547, http://dx.doi.org/10.1107/S1600577515016604.


Bowler, M.W., Svensson, O. & Nurizzo, D. (2016): Fully automatic 
macromolecular crystallography: the impact of MASSIF-1 on the optimum 
acquisition and quality of data, Crystallography Reviews, 
http://dx.doi.org/10.1080/0889311X.2016.1155050.


Nurizzo, D., Bowler M.W., et al. (2016) RoboDiff: combining a sample 
changer and goniometer for highly automated macromolecular 
crystallography experiments Acta Cryst D72, 966-975, 
http://dx.doi.org/10.1107/S205979831601158X


For any further questions please don't hesitate to contact me 
(mbow...@embl.fr) or Didier Nurizzo (nuri...@esrf.fr).


Best wishes, Matthew.

Web:http://www.esrf.eu/MASSIF1
Mail: mass...@esrf.fr
FAQ:http://www.esrf.eu/MASSIF_FAQ


--
Matthew Bowler
Synchrotron Crystallography Group
European Molecular Biology Laboratory
71 avenue des Martyrs
CS 90181 F-38042 Grenoble
France
===
Tel: +33 (0) 4.76.20.76.37
Fax: +33 (0) 4.76.20.71.99

http://www.embl.fr/
http://www.esrf.eu/MASSIF1
https://twitter.com/id30_massif1
http://www.embl.fr/research/unit/mccarthy/members/index.php?s_personId=CP-60015559
===

[ccp4bb] Conserved water

[gerardo andres]

Hi everyone, does anyone know any strategy or program (besides pywater) to 
identify conserved waters in a protein?
Thanks, 
Gerardo

[ccp4bb] RCSB PDB looking for Postdoctoral Fellows to join our multidisciplinary development team at UC San Diego

[Christine Zardecki]

The Challenge: Develop innovative analysis, integration, query, and 
visualization tools for 3D biomolecular structures to help accelerate research 
and training in biology, medicine, and related disciplines. In these projects, 
we employ the latest advances in computer science to develop highly interactive 
features and scalable services and workflows. The overall goal is always to 
develop highly interactive features for the RCSB PDB website.

Two Postdoctoral Fellow positions are available: one focused on Visualization 
(position #1104 ) 
and Machine Learning/Biological Assemblies (position #1105 
). Possible 
project areas include:

Innovative representations for 3D structural data, including biological 
assemblies
Visualizations for comparative analyses
Multiscale rendering for exploring large structures
Using machine learning to build the next generation search engine for molecular 
biology
This is a unique opportunity to engage in leading edge research, development, 
and outreach activities of the RCSB PDB with worldwide impact. 

For more information, contact us at 
http://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/contact/job_listings.html


--
Twitter: http://twitter.com/#!/buildmodels
Facebook:  http://www.facebook.com/RCSBPDB

Re: [ccp4bb] AW: [ccp4bb] Molecular replacement with template having low sequence identity

[Eleanor Dodson]

Please tell us what worked.
Eleanor

On 6 June 2017 at 04:52, Shankar Prasad Kanaujia 
wrote:

> Dear All,
>
> I am very happy to inform you that I have finally solved the structure.
> Thanks to all for your kind suggestions.
>
> With best regards,
> Shankar
>
> On Wed, Aug 3, 2016 at 8:35 PM, Sudipta Bhattacharyya <
> sudiptabhattacharyya.iit...@gmail.com> wrote:
>
>> Dear Shankar,
>>
>> The high TFZ and LLG you mentioned indeed indicate a possible solution.
>> However, how certain are you about the number of ensembles placed in the
>> ASU? Also this high Rfree value sometime indicates the presence of
>> t-NCS/twining, Did you check that (the presence of large off origin t-NCS
>> peak)? Although phaser should detect it and correct it accordingly but only
>> if you are searching for even number of ensembles in the ASU.
>>
>> Good luck,
>> Sudipta.
>>
>> On Wed, Aug 3, 2016 at 9:14 AM, Shankar Prasad Kanaujia <
>> spkanau...@gmail.com> wrote:
>>
>>> Dear All,
>>>
>>> As suggested, I tried several things. I am getting MR solutions with TFZ
>>> > 8.0 (e.g. 12, 16) and high LLG (e.g. 150, 160). However, Rw/Rf remains
>>> above 0.50 after first round of refinement. In some cases, after some
>>> manual model building, Rw falls up to 0.46, however, Rf remains above 0.50.
>>>
>>> Any suggestions for further model building. The data is of ~1.9 Angst
>>> processed in P1211.
>>>
>>> With best regards,
>>> Shankar
>>>
>>> On Mon, Aug 1, 2016 at 1:48 PM,  wrote:
>>>
 Dear Schankar,



 you could also try automatic packages like Balbes or Morda. However, it
 might not be a bad idea to try a more rational approach as well. With 27%
 sequence identity, you template may or may not have the same fold. With 27%
 sequence identity AND a similar biological function (e.g. similar reaction
 catalysed, binding to a similar receptor etc.), your bets are much better.
 (Except cases with large conformational changes like antibodies and
 calmodulin).



 If molecular replacement fails, you should also look very carefully in
 the space group assignment and in case of ambiguity try all possible space
 groups for your MR searches.



 Best,

 Herman







 *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag
 von *Sivakumar N
 *Gesendet:* Montag, 1. August 2016 08:30
 *An:* CCP4BB@JISCMAIL.AC.UK
 *Betreff:* Re: [ccp4bb] Molecular replacement with template having low
 sequence identity



 Dear Shankar,

 How do you appreciate this approach of generating an Ensemble of
 superposed homologous structures as a MR search probe? I found the FUGUE
 server helpful in pulling out the distantly related structural homologues
 for a given query sequence.  Also, a manual or an automated method of
 refining or sieving the superposed homologues to cut out the residues that
 fall in the loop regions and possibly other residues at loci that introduce
 any noisy-correspondences between the superposed structures can be useful,
 in order to arrive at a better RMSD values between the equivalent Cα atoms
 of this hybrid MR search probe.

 Regards

 Sivakumar,N.



 On Sat, Jul 30, 2016 at 6:20 PM, Shankar Prasad Kanaujia <
 spkanau...@gmail.com> wrote:

 Dear All,

 Is it possible to solve the structure of a protein having template with
 a sequence identity of 27%. If yes, what is the best possible method.

 Any program which can automatically give some clue.

 With best regards,

 Shankar



>>>
>>>
>>>
>>> --
>>> Shankar Prasad Kanaujia, Ph.D.
>>> Assistant Professor
>>> Department of Biosciences and Bioengineering
>>> Indian Institute of Technology Guwahati
>>> Guwahati - 781039 Assam, India
>>> Tele: 0361 258 2228
>>> Fax:  0361 258 2249
>>> Email: spkanau...@iitg.ernet.in
>>> Homepage: http://www.iitg.ernet.in/spkanaujia/
>>> Google Scholar: https://scholar.google.com/cit
>>> ations?user=Zt4JSNYJ=en
>>>
>>
>>
>
>
> --
> Shankar Prasad Kanaujia, Ph.D.
> Associate Professor
> Department of Biosciences and Bioengineering
> Indian Institute of Technology Guwahati
> Guwahati - 781039 Assam, India
> Tele: 0361 258 2228
> Fax:  0361 258 2249
> Email: spkanau...@iitg.ernet.in
> Homepage: http://www.iitg.ernet.in/spkanaujia/
> Google Scholar: https://scholar.google.com/citations?user=Zt4JSNYJ;
> hl=en
>

[ccp4bb] Release of the latest version of SPHIRE

[Stefan Raunser]

Dear EM community,
We are excited to announce the release of the latest version of our SPHIRE  
software suite (SPHIRE Beta Patch 1) (co-distributed with EMAN 2.2 and SPARX) , 
which is now available from our website:

http://sphire.mpg.de

Main new components and updates:

- ISAC2 – Rapid and stable 2D Clustering
We optimized the popular ISAC algorithm for 2D Clustering (Yang et al., 
Structure, 2012). ISAC yields now validated 2D class averages > 10-15x faster 
than before.
In addition, the new Beautifier tool allows further refinement and sharpening 
of the ISAC 2D class averages in order to reveal high-resolution features in 2D.

- MERIDIEN – Rapid ML 3D Refinement
We introduced the polar coordinates methodology (Penczek et al., 1992) and 
optimized the parallelization of the program to speed up the structure 
refinement, reduce the memory requirements and enable calculation on single 
nodes.
MERIDIEN is now > 10-15x faster than the previous version.
Cryo-EM structure determination with SPHIRE is now possible within a few days 
on small clusters and desktop machines.

- RSORT3D – Reproducible 3D sorting
We re-implemented and improved the 3D sorting procedure and methodology. The 
updated RSORT3D is 3-4x faster and capable to run on desktop machines.  More 
importantly, it produced better results for several high resolution projects in 
our lab.

- Icosahedral, Tetrahedral and Octahedral Symmetry
Refinement of particles with icosahedral, tetrahedral, and octahedral 
symmetries is now supported.

- Easy installation
The release of SPHIRE Beta Patch 1 is synchronized with the release of EMAN 
2.2. The new Anaconda Installer allows a fast and smooth co-installation of 
both programs. At the moment we only support CentOS, but we work hard on 
developing a MacOS Installer for the upcoming stable release.

For any issues and inquiries, the SPHIRE team is accessible almost 24/7 via the 
mailing 
list.
We sincerely hope that the updated SPHIRE Beta Patch 1 version will meet your 
expectations and be a helpful advance in high-resolution cryo-EM.

Your SPHIRE development team

Toshio, Markus, Felipe, Thorsten, Michael, Christos, and Stefan – MPI Dortmund

Zhong and Pawel - UTH Texas

(Follow us on Twitter: https://twitter.com/SPHIRE_Package)

-
Stefan Raunser, Ph.D.

Director, Department of Structural Biochemistry
Max Planck Institute of Molecular Physiology
Otto-Hahn-Str. 11
44227 Dortmund, Germany
tel: +49-231-133-2300

and

Adjunct Professor, Faculty of Chemistry and Chemical Biology
Technical University Dortmund

Honorary Professor, Centre for Medical Biotechnology, Faculty of Biology
University Duisburg-Essen