Re: [ccp4bb] CCP4 Release 6.5

[Eugene Krissinel]

> Does this mean I need to download the installation package from the CCP4

- yes

> and is this why the update tool in 6.4.0 is not showing up the latest release?

- no, this must be something different

> Should I install into the current 6.4.0 directory or a new one?

- some CCP4 components rely on CCP4 directory name to be correct. It is 
therefore advisable to keep it as suggested by CCP4 installer/tarball, which is 
‘ccp4-6.5’ for this release

> Will my existing data folders etc. be retained?

- you should be able to see all your data and projects in ccp4i after upgrade; 
I do not remember reports on lost data due to CCP4 upgrade from users :)

Best regards,

Eugene



> 
> Thanks.
> Mohamed
> 
> On 18/12/2014 21:54, Eugene Krissinel wrote:
>> Dear CCP4 Users,
>> 
>> 
>> 
>> The CCP4 Core Group is very pleased to announce the release of the latest 
>> version of the CCP4 Software Suite. Version 6.5 (Hellifield) is now 
>> available from the CCP4 download website:
>> 
>> 
>> 
>> http://www.ccp4.ac.uk/download.php
>> 
>> 
>> 
>> The release is available for Linux, Mac OSX and Windows platforms. This 
>> release mostly consolidates updates in CCP4 6.4.0 update series, but also 
>> introduces a number of technical improvements and new features.
>> 
>> 
>> 
>> The whys and wherefores:
>> 
>> 
>> 
>> Why is it necessary to switch to CCP4 6.5 now?
>> 
>> a)  Because it brings new features and updates
>> 
>> b)  Because the update line of 6.4.0 is now discontinued
>> 
>> c)  Because support for 6.4.0, as well as for all earlier versions of CCP4, 
>> is now stopped.
>> 
>> 
>> 
>> Why did CCP4 make a new release rather than keeping on updating the current 
>> one?
>> 
>> Because over the last year, the difference between the release and the 
>> development (trunk) branches of CCP4 has reached a point where merging them 
>> takes a considerable effort and makes updates unfeasible.
>> 
>> 
>> 
>> Why 6.5 and not 6.5.0?
>> 
>> Because the last numeral will be now defined by the last CCP4 update applied 
>> (not to worry, updates will not change the CCP4 directory name, which will 
>> remain ‘ccp4-6.5’ for the lifetime of the release). The full version number 
>> (including updates) will be printed on top of all the log files.
>> 
>> 
>> 
>> 
>> 
>> 1. New Components and Updates
>> 
>> 
>> 
>> Below is a selected list of updates and new components; for more details 
>> please see the individual program documentation.
>> 
>> 
>> 
>> New:
>> 
>> 
>> 
>> Privateer-validate: validation of carbohydrate structures from Jon Agirre 
>> (The University of York)
>> 
>> -   Calculates the conformation of pyranoses and furanoses using the 
>> Cremer-Pople algorithm.
>> 
>> -   Compares the detected conformation to the minimal-energy conformation of 
>> the sugar.
>> 
>> -   Performs basic stereochemistry and geometry checks.
>> 
>> -   Computes a real space correlation coefficient against a positive omit 
>> density. Outputs 2mFo-DFc, mFo-DFc and omit mFo-DFc maps.
>> 
>> -   Describes N- and O-glycan structures.
>> 
>> 
>> 
>> Feckless: combination of multilattice files from Mosflm for Pointless & 
>> Aimless, from Phil Evans (MRC/LMB).
>> 
>> 
>> 
>> Acedrg v90 and LibG: chemoinformatics support for Refmac (geometry and 
>> restraint generator), from Garib Murshudov’s team at MRC/LMB.
>> 
>> 
>> 
>> Blend v0.5.10: optimum selection of multi-crystal datasets for merging from 
>> James Foadi, MPL, Harwell, UK
>> 
>> -   suggests favourable or desirable combinations of datasets
>> 
>> -   provides tools for easy management of multi-crystal operations
>> 
>> -   reads in integrated data from MOSFLM or XDS
>> 
>> -   outputs scaled data and associated statistics using POINTLESS and AIMLESS
>> 
>> 
>> 
>> Crank-2: conceptually redesigned and considerably improved Crank pipeline 
>> for automatic experimental phasing from Navraj Pannu and Pavol Skubak, 
>> University of Leiden, The Netherlands.
>> 
>> 
>> 
>> 
>> 
>> Updated:
>> 
>> 
>> 
>> Aimless v0.5.1 (Scaling multiple observations of reflections)
>> 
>> -   some options for XFEL data (SAMPLESD, Rsplit, batch rejection)
>> 
>> -   use estimated scale parameter errors in sigma(I); improved SDcorrection
>> 
>> -   CC(1/2) maximum resolution from curve fit
>> 
>> -   matrix of run-run correlations
>> 
>> 
>> 
>> Pointless v1.9.23 (Laue group determination)
>> 
>> -   bug fixes
>> 
>> 
>> 
>> Prosmart v0.845 (Macromolecular restraints generator)
>> 
>> -   Enabled structural comparison and restraint generation functionalities 
>> with DNA/RNA chains
>> 
>> -   Ability to calculate and display screw axis-angle representation 
>> corresponding to rigid-body transformations
>> 
>> -   Support for UCSF Chimera
>> 
>> -   Various technical enhancements and changes to default 
>> parameters/behaviour
>> 
>> 
>> 
>> Buccaneer v1.6.0 (Model autobuilding)
>> 
>> -   new modes for building after molecular replacement, with facilities for 
>> differing levels of data quality and model agre

[ccp4bb] Cross-validation when test set is miniscule

[Derek Logan]

Hi everyone,

Right now we have one of those very difficult Rfree situations where it's 
impossible to generate a single meaningful Rfree set. Since we're in a bit of a 
hurry with this structure it would be good if someone could point me in the 
right direction. We have crystals with 1542 non-H atoms in the asymmetric unit 
that diffract to only 3.6 Å in P65, which gives us a whopping 2300 reflections 
in total. 5% of this is only about 100 reflections. Luckily the protein is only 
a single point mutation of a wild type that has been solved to much better 
resolution, so we know what it should look like and I simply want to 
investigate the effect of different levels of conservatism in the refinement, 
e.g. NCS in xyz and B, group B-factors, reference model, Ramachandran 
restraints etc. However since the quality criterion for this is Rfree I'm not 
able to do this.

I believe the correct approach is k-fold statistical cross-validation, but can 
someone remind me of the correct way to do this? I've done a bit of Googling 
without finding anything very helpful.

Thanks
Derek

Derek Logan tel: +46 46 222 1443
Associate Professor mob: +46 76 8585 707
Dept. of Biochemistry and Structural Biology  
www.cmps.lu.se
Centre for Molecular Protein Sciencewww.maxlab.lu.se/crystal
Lund University, Box 124, 221 00 Lund, Sweden   www.saromics.com

[ccp4bb] XDS and XDSGUI latest versions

[Kay Diederichs]

Hi everybody,

pls note that the XDS version that you might have installed a year ago
will expire on Dec 31, and there's a new version at
http://xds.mpimf-heidelberg.mpg.de/ . The changes are: support for
Eiger, support for XZ compressed files, and assorted small fixes.

The XDS documentation is still being improved, e.g.
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Problems#IDXREF_produces_too_short_cell_parameter.28s.29

Furthermore the latest version of XDSGUI is documented in the XDSwiki
(http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSGUI), and
the download links for Linux and Mac are provided there. I'm still
trying to find the easiest way to install XDS and related programs, and
I'd particularly appreciate help with a Mac installer that would package
xds-viewer, xdsstat, generate_XDS.INP and xdsgui. Some stuff that may be
helpful is in the "Installation" article in XDSwiki.

best wishes,

Kay
-- 
Kay Diederichshttp://strucbio.biologie.uni-konstanz.de
email: kay.diederi...@uni-konstanz.deTel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz

This e-mail is digitally signed. If your e-mail client does not have the
necessary capabilities, just ignore the attached signature "smime.p7s".

[ccp4bb] Postdoctoral Fellow Position – Structural Biology at Rutgers University School of Dental Medicine

[Vijay Parashar]

A postdoctoral position is available immediately in the Department of Oral 
Biology Rutgers School of Dental Medicine for a highly motivated, creative 
individual with strong interest in the structure and function of proteins 
regulating bacterial signaling. The ideal candidate will have a strong 
background in macromolecular X-ray crystallography, biochemistry, protein 
purification, and molecular biology. A working knowledge of bacterial genetics 
and computational modeling of protein-ligand interactions is a plus. Candidates 
with demonstrated success in another field and a strong commitment to learning 
the crystallographic process will also be considered.
The Rutgers University Newark campus is well equipped with state-of-the-art 
equipment for molecular biology, protein biochemistry, and crystallography, 
including crystallization robot, and X-ray generator.
Applicants should send a cover letter, a CV, a list of publications, a detailed 
summary of research experience and interests as well as the names and contact 
information of three references. The information should be sent via e-mail to 
paras...@sdm.rutgers.edu with the subject line “Postdoctoral Position 
Applicant”. The Rutgers University is an Equal Opportunity/Affirmative Action 
Employer.
 

Thanks,
Vijay

[ccp4bb] Announcement - 5th Winter School on Soft X-rays in Macromolecular Crystallography

[Bi-Cheng Wang]

Sent on behalf of the Organizing Committee:	John Rose, Manfred Weiss, Christoph Mueller-Dieckmann and B.C. WangThe 5th Winter School on Soft X-Rays in Macromolecular Crystallography	Location:	Georgia Center, The University of Georgia, Athens, Georgia, USA 30602	Dates:	March 1 - 4, 2015The 5th Winter School on Soft X-rays in Macromolecular
Crystallography is a continuation of similar activities that have been held in
Europe every three-years since 2003 as indicated below.	1st Winter School: Bressanone/Brixen, Italy; Feb.
25-27, 2003	2nd Winter School: Seefeld, Austria; March 22-25, 2006	3rd Winter School: Berlin, Germany; February 18-20,
2009	4th Winter School: Grenoble, France, February 6-8, 2012The 5th Winter Scholar will be held at the University
of Georgia, Athens, Georgia, USA from March 1 to 4, 2015 (http://wssxmc.bmb.uga.edu).  Applications are open
to all interested researchers.  Travel Awards are available for US & international young scientists. Important Deadlines:		February 2, 2015 	- Travel Award Application Submission	February 2, 2015 	- Hotel Reservations at UGA Hotel & Conference Center	February 15, 2015	- Online Registration
for the Winter School	February 15,
2015 	-
Abstract SubmissionA tentative Course Schedule is attached.

Winter School_Tentative_Schedule_141218.pdf
Description: Adobe PDF document

[ccp4bb] WCPCW registration and deadline

[Nathan Henderson]

Reposted here on behalf of the organizing committee:

Dear Potential Attendees of the 2015 West Coast Protein Crystallography 
Workshop,

To register for the 22nd WCPCW (March 15 - 18, 2015, Monterey, CA), please 
visit:
http://www.wcpcw2015.info/registration--2.html
Standard registration will close on Jan. 20, 2015.  Registration provides you 
with lodging from Sunday night (March 15th) to Wednesday morning (March 18th).
A tentative conference schedule is available at:
http://www.wcpcw2015.info/schedule.html

Some of you have inquired about booking additional nights at the Monterey Plaza 
Hotel prior to the start and after the conclusion of the conference.  If you 
wish to extend your stay, please register for the conference first, then 
contact the hotel directly and let them know you are with the West Coast 
Protein Crystallography Workshop.

Monterey Plaza Additional Reservations:
1-800-334-3999, extension: #2
Conference Rate for Inland Rooms: $165.00 plus taxes
Conference Rate for Ocean View Rooms (no balcony): $235.00 plus taxes
(***Please note that these room rates are only available to those who have 
already registered for the conference through our system***).

Looking forward to seeing you all, your conference chair,
Rebekka
__
Rebekka Wachter, Associate Professor
Department of Chemistry and Biochemistry
Center for Bioenergy and Photosynthesis
Center for Membrane Proteins in Infectious Disease
Arizona State University
Email: rwach...@asu.edu
Phone: 480-965-8188
Fax: 480-965-2747
http://chemistry.asu.edu/faculty/r_wachter.asp

[ccp4bb] WCPCW timelines

[Nathan Henderson]

Reposted here on behalf of the organizing committee:

All,

Please note our updated timelines:

October 20, 2015: Standard Registration opens
January 20, 2015: Standard Registration closes
January 21, 2015: Late Registration opens (accommodations cannot be guaranteed)
January 23, 2015: Deadline for Abstract submission

Refund Policy:
Before February 20, 2015: 50% refund upon request.
We will not be able to give any refunds after February 20, 2015 (5:00 pm).

For more information, please visit the conference web site:
http://www.wcpcw2015.info/home.html

Looking forward to seeing you all,
Your chair Rebekka

__
Rebekka Wachter, Associate Professor
Department of Chemistry and Biochemistry
Center for Bioenergy and Photosynthesis
Center for Membrane Proteins in Infectious Disease
Arizona State University
Email: rwach...@asu.edu
Phone: 480-965-8188
Fax: 480-965-2747
http://chemistry.asu.edu/faculty/r_wachter.asp

[ccp4bb] Cross-validation when test set is miniscule

[dusan turk]

Dear Derek,

I suggest you not not use the cross validation at all. With small data sets the 
refinement with cross validation is very unstable and the choice of the TEST 
set dependent. We explained why and suggested to use an alternative function, 
which can use all data in refinement.

Acta Cryst. (2014). D70, 3124-3134  [ doi:10.1107/S1399004714021336 
 ]
Free kick instead of cross-validation in maximum-likelihood refinement of 
macromolecular crystal structures

J. Praznikar 

 and D. Turk 

Synopsis: The maximum-likelihood free-kick target, which calculates model error 
estimates from the work set and a randomly displaced model, proved superior in 
the accuracy and consistency of refinement of crystal structures compared with 
the maximum-likelihood cross-validation target, which calculates error 
estimates from the test set and the unperturbed model.

Online 22 November 2014

best regards,
dusan


> On Dec 20, 2014, at 1:05 AM, CCP4BB automatic digest system 
>  wrote:
> 
> Date:Fri, 19 Dec 2014 11:18:37 +
> From:Derek Logan  >
> Subject: Cross-validation when test set is miniscule
> 
> Hi everyone,
> 
> Right now we have one of those very difficult Rfree situations where it's 
> impossible to generate a single meaningful Rfree set. Since we're in a bit of 
> a hurry with this structure it would be good if someone could point me in the 
> right direction. We have crystals with 1542 non-H atoms in the asymmetric 
> unit that diffract to only 3.6 Å in P65, which gives us a whopping 2300 
> reflections in total. 5% of this is only about 100 reflections. Luckily the 
> protein is only a single point mutation of a wild type that has been solved 
> to much better resolution, so we know what it should look like and I simply 
> want to investigate the effect of different levels of conservatism in the 
> refinement, e.g. NCS in xyz and B, group B-factors, reference model, 
> Ramachandran restraints etc. However since the quality criterion for this is 
> Rfree I'm not able to do this.
> 
> I believe the correct approach is k-fold statistical cross-validation, but 
> can someone remind me of the correct way to do this? I've done a bit of 
> Googling without finding anything very helpful.
> 
> Thanks
> Derek
> 
> Derek Logan tel: +46 46 222 1443
> Associate Professor mob: +46 76 8585 707
> Dept. of Biochemistry and Structural Biology  www.cmps.lu.se 
> >
> Centre for Molecular Protein Sciencewww.maxlab.lu.se/crystal 
> 
> Lund University, Box 124, 221 00 Lund, Sweden   www.saromics.com 
> 

Dr. Dusan Turk, Prof.
Head of Structural Biology Group http://bio.ijs.si/sbl/ 
 
Head of Centre for Protein  and Structure Production
Centre of excellence for Integrated Approaches in Chemistry and Biology of 
Proteins, Scientific Director
http://www.cipkebip.org/
Professor of Structural Biology at IPS "Jozef Stefan"
e-mail: dusan.t...@ijs.si
phone: +386 1 477 3857   Dept. of Biochem.& Mol.& Struct. Biol.
fax:   +386 1 477 3984   Jozef Stefan Institute
Jamova 39, 1 000 Ljubljana,Slovenia
Skype: dusan.turk (voice over internet: www.skype.com