Directories & Projects Spring Cleaning

From: mark Mayer
Date: 7 March 2012 18:55


I'd appreciate suggestions about how to reorganize my My Directories&ProjectDir listing.
Its currently got several years worth of work and is getting hard to work with.
I'd like to archive old projects (say by year) but keep all the CCP4i files for each project intact, so that I can easily go back to them in the future without having to wade through the current multi year list.

Thanks

----------
From: Enrico Stura

Mark,

I am faced with the same problem. I work under Linux.
Since everything depends from the .CCP4 directory,
 this directory  can be copied to
a storage location. Example: /oldproj/dotCCP4_2011:
/home/user % cp -r .CCP4   /oldproj/dotCCP4_2011

Once this directory has been effectively backed up
all old projects can be deleted in the ccp4i interface.
The Spring cleaned .CCP4 can be moved
to a new location for example: /projects/dotCCP4_2012
/home/user % mv .CCP4  /projects/dotCCP4_2012
A logical link is established with:
/home/user % ln -s /projects/dotCCP4_2012 .CCP4
The link will point to the new directory. This new directory
will be filled up during 2012 and at the end of the year
backed up in the same way.

To re-use old environments:
/home/user % ln -s /oldproj/dotCCP4_2011 .CCP4
Will allow to return to the 2011 status.

As long as nothing is deleted, nothing is lost.
Caution: Transfered directories may need logical links to ensure that
connectivity to the directories is maintained.

This is not very elegant and I do this by hand since I am not aware of any
script that does it automatically.
Probably in a future version of ccp4i there will be an archive function.
I am sure that many other users would wlecome it too.


Enrico.

CALL FOR PROPOSALS: neutron beam time at the Protein Crystallography Station at LANL

From: Suzanne Zoe Fisher
Date: 2 May 2012 22:30

Dear Colleague,

The Protein Crystallography Station is a high performance neutron beamline located at the spallation neutron source at the Los Alamos Neutron Science Center in Los Alamos, NM. We are also pleased to announce that our in-house X-ray diffractometer is installed and available for user experiments as well. We also offer full support for perdeuterared protein expression, purification, and crystallization. The PCS routinely collects data on H/D exchanged samples and perdeuteration is not a requirement.

We are accepting proposals for our neutron beam run cycle starting 4th August and running until late December 2012. 

We strongly encourage you to contact the instrument scientists for questions concerning sample preparation, instrument capabilities, sample environments, and/or proposal preparation:

Beamline scientist: Zoë Fisher zfisherATlanl.gov
or Andrey Kovalevsky aykATlanl.gov

PROPOSAL GUIDANCE AND SUBMISSION
Proposals may be submitted by clicking on the "Submit Proposal" link in the left column of the Lujan home page http://lansce.lanl.gov/lujan/index.shtml    

When accessing the proposal submission site for the first time, use your e-mail address as the "Username" and click on the "forgot password" button.  You will be sent a link by email to set your new password.  After logging in, fill out or update your personal information. When you hit "save and continue", you will be directed to the first proposal submission page. 

Check out the references below for exciting updates from our beamline:

- Chen et al. (2012) Room temperature ultra high resolution neutron and x-ray diffraction studies of H/D-exchanged crambin, Acta Crystallogr. D68, p.119-123.

       http://www.ncbi.nlm.nih.gov/pubmed/22297981

- Fisher et al. (2011) Neutron structure of human carbonic anhydrase II: a hydrogen-bonded water network "switch" is observed between pH 7.8 and 10.0, Biochemistry 50, p.9421-9423.

      http://www.ncbi.nlm.nih.gov/pubmed/21988105

- Kovalevsky et al. (2011) identification of the elusive hydronium ion (H3O+) exchanging roles with a proton in an enzyme at lower pH values, Angewandte Chemie 50, p.7520-7523.

      http://www.ncbi.nlm.nih.gov/pubmed/21604345

Beamline Scientist (I03) position available at DIAMOND

From: Katherine McAuley
Date: 3 May 2012 14:00

Dear all,

Following from Martin's post yesterday, we also have a beamline scientist vacancy at Diamond to join the I03 beamline team. I03 provides a facility for the determination of biological macromolecules using X-ray diffraction. The beamline is equipped with a state of the art experimental end-station which can be operated to work with hazard group 3 pathogens.

This vacancy offers an exciting opportunity to be involved in the development of the unique infrastructure that I03 will provide to the user community. The successful candidate will also be expected to develop an internationally competitive research programme in structural biology that complements the research and development activities within the MX village.

Full details of the post and how to apply can be found here:

http://www.diamond.ac.uk/Home/Jobs/Current/DIA0731_TH.html

Informal inquires can be directed to Katherine McAuley either by telephone or by email: katherine.mcauleyATdiamond.ac.uk.

The closing date is 31^st May 2012 and interviews will be held on 13^th June.

Best Regards,

Katherine

PhD Position at the Institut de Biologie Structurale Jean-Pierre Ebel Grenoble

From: Monika Spano
Date: 3 May 2012 15:37

PhD Position at the Institut de Biologie Structurale Jean-Pierre Ebel Grenoble

A PhD position is available in the Synchrotron Group headed by Dr Jean-Luc Ferrer at the Institut de Biologie Structurale (IBS) at Grenoble, starting in Autumn 2012. IBS is close to the European large instruments, the ILL and the ESRF. The project aims at developing an automated microfluidic pipeline for protein crystallization. It combines the control of temperature and precipitant concentration in a user-friendly setup allowing for screening in microfluidic chips, in situ diffraction screening, and systematic optimization based on the phase diagram and finally reliable mounting of crystals for data collection. The pipeline consists of three elements: the microchip for screening, the optimization platform and robotic crystal mounting.

We are looking for an enthusiastic academically qualified physicist, chemist or engineer with a strong interest in structural biology. The candidate should have affinity to multi-disciplinary problems. Experience in macromolecular crystallization and/or crystallography is welcome. Given the scope of the project and the need for a close collaboration with the other team members as well as with the industrial/external partners excellent communicative skills and the ability to work in a team with biologists and engineers are prerequisites.

More information on the PhD position can be obtained from:

Monika Budayova-Spano, PhD

Assistant Professor, Faculty of Pharmacy, University Joseph Fourier

Tel: + 33 4 38 78 96 13

Fax: + 33 4 38 78 51 22

Email: Monika.Spano AT ibs.fr

For application please supply the following: a detailed resume, a covering letter explaining the applicant's motivation for the position, detailed exam results, two references : the name and contact details of at least two people who could be contacted to provide an appreciation of the candidat. Please, send it to monika.spano AT ibs.fr and to jean-luc.ferrer AT ibs.fr.

___________________________________

Crystallographer - Principal Beamline Scientist (I04-1) position available at DIAMOND

From: Martin Walsh
Date: 2 May 2012 11:20

Dear all,

We are in the process of recruiting a Senior Scientist at Diamond with responsibility for the MX beamline I04-1 which forms part of the MX village suite.

This provides an exciting opportunity to lead the operation and development of I04-1 through the direct management of a small team of scientists and interactions with the other four currently operational beamlines within the MX village at Diamond (http://www.diamond.ac.uk/Home/Beamlines/MX.html). 

 

The Principal Beamline Scientist is expected to establish an internationally competitive research programme that complements the activities of the MX village (Structural biology, Crystallographic methods development and/or Instrumentation). To this end Diamond provides state of the art facilities for all aspects of structural biology and will fund a full time post-doctoral research associate, as well as supporting graduate students through sponsorship with academic institutions via the Diamond PhD studentship programme.

 

Full details of the post and how to apply can be found here:

http://www.diamond.ac.uk/Home/Jobs/Current/DIA0732_TH.html

 

Informal inquires about the post can be directed directly to Martin Walsh

 

The closing date is set at 2/6/2012

Martin

 

Workshop on Advanced Topics in EM Structure Determination

From: Clint Potter
Date: 2 May 2012 21:00


The National Resource for Automated Molecular Microscopy

Announces

A Workshop on Advanced Topics in EM Structure Determination

November 11-16, 2012

National Resource for Automated Molecular Microscopy
The Scripps Research Institute (TSRI), La Jolla, California.

We invite applications to participate in a Workshop on EM Structure Determination of Challenging Macromolecules.  The workshop is aimed at students, postdocs and faculty that already have some experience practicing cryoEM.  We can accommodate a total of 100 participants.

A major goal of the workshop will be to discuss some of the challenges that we face in using cryoEM to solve the structure of macromolecules.  Topics to be discussed will include improvements in specimen preparation, imaging, processing and reconstruction, and methods for validation. The basic format of the course will be theoretical lectures in the mornings followed by practical demonstrations and panel discussions in the afternoon. Evenings will be reserved for poster presentations by participants and research talks by instructors.

The instructors for the course will include: Yifan Cheng (UCSF), Wah Chiu (Baylor), David DeRosier (Brandeis), Joachim Frank (Columbia), Bob Glaeser (LBL), Niko Grigorieff (Brandeis), Richard Henderson (MRC), Tilak Jain (TSRI), Gabe Lander (Berkeley), Steve Ludtke (Baylor), Pawel Penczek (U. Texas- Houston), John Rubinstein (Hospital for Sick Children, Toronto), Sjors Scheres (MRC), Holger Stark (Max Planck- Göttingen), Elizabeth Villa (MPI), and Tom Walz (Harvard).

Application forms may be found online at the workshop web page:
http://nramm.scripps.edu/?page_id=2424

A registration fee of $750 will be charged to participants from non-profit institutions. Some partial scholarship support may be available depending on the success of efforts to raise support. All meals will be provided as part of the workshop registration fee but participants will be expected to cover their own travel and lodging expenses. Cost of housing is estimated to be under $100/night for a shared room and transportation will be provided between the hotel and the workshop venue.  Further details on these and other matters will be provided once the registration process begins.

The application deadline is 1 July and a final selection of participants will be made by 15 August.

Please see all other information pertaining to the course at the web site:
http://nramm.scripps.edu/?page_id=2424



Organizers
Bridget Carragher, Clinton S. Potter and Ronald A. Milligan
National Resource for Automated Molecular Microscopy,
The Scripps Research Institute

The National Resource for Automated Molecular Microscopy is supported by grants from the National Institute of General Medical Sciences (GM103310).

MAMCM reminder

From: David R. Cooper
Date: 27 April 2012 21:23

The 42nd Mid-Atlantic Macromolecular Crystallography meeting will be held at the University of Virginia from May 31 – June 2, 2012.  There are several reasons why you should make your plans now!  Most of the blocks of hotel rooms will be released to the public  and conference rates will expire on Monday, April 30th, 2012.  Also, after Monday University Housing will charge a $50 late registration fee. Additionally, space is limited for the Saturday workshops, and slots are filling up.

Details of the meeting can be found at http://www.mid-atlantic.org/ .

We are also excited to announce TWO $250 poster prizes, one for students and one for postdocs!

Respectfully,
Drs. David Cooper, Peter Horanyi and Michael Purdy
Co-Directors of the 42nd MAMCM
http://www.mid-atlantic.org

We would like to thank our sponsors: Agilent Technologies Inc., Art Robbins Instruments, Bruker, Emerald BioSystems, Formulatrix, HKL Research Inc., Labcyte, MiTeGen, Rigaku Americas Corporation, Rockland Immunochemicals, and TTP LabTech.

problem with coot install

From: Alexander U. Singer
Date: 13 February 2012 21:17


Hi -- I was installing the latest version of CCP4 6.2.0 on my machine which uses Linux Fedora Core 5.  When downloading the CCP4 package, I used the 'generic linux (x86) option'.  The package contains an package for Coot v 0.6.2 which I tar'ed and uncompressed, but when I try to run it, I get this error

./coot-real
./coot-real: error while loading shared libraries: libgio-2.0.so.0: cannot open shared object file: No such file or directory
./coot: line 254: 16409 Floating point exception$COOT_PREFIX/bin/guile -s $COOT_PREFIX/share/coot/scheme/coot-crash-catcher.scm $coot_real $*

Do you know how I can overcome this problem?

Thanks for your help

Alex Singer
--

----------
From: Paul Emsley

On 14/02/12 08:17, Alexander U. Singer wrote:

Hi -- I was installing the latest version of CCP4 6.2.0 on my machine
which uses Linux Fedora Core 5.  When downloading the CCP4 package, I
used the 'generic linux (x86) option'.  The package contains an
package for Coot v 0.6.2 which I tar'ed and uncompressed, but when I
try to run it, I get this error

./coot-real
./coot-real: error while loading shared libraries: libgio-2.0.so.0:
cannot open shared object file: No such file or directory
./coot: line 254: 16409 Floating point exception$COOT_PREFIX/bin/guile
-s $COOT_PREFIX/share/coot/scheme/coot-crash-catcher.scm $coot_real $*

Do you know how I can overcome this problem?

I guess you need to install the library.

For me it's in the following package

glib2-devel-2.28.8-1.fc15.x86_64.

Either that, or you need a binary that has older dependencies.

It's unusual for an .so not to be a link (used by developers).  I am surprised that the binary you are using is linked to an .so.

FC5 is pretty ancient these days.

Paul.

----------
From: Bernhard Rupp (Hofkristallrat a.D.)


It might be worthwhile to follow the thread of similar problems on the coot
mailing list
and a generic solution on the coot-wiki, like

http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Example:_in
stalling_a_64bit_nightly_CentOS5_binary_build_on_64bit_SL6.1

BR

Computation Crystallography Newsletter

From: Nigel Moriarty
Date: 14 February 2012 19:27


Folks

The latest issue of the Computational Crystallography Newsletter is
available on-line at http://www.phenix-online.org/newsletter for
download. The articles are of general interest to protein
crystallographers and are listed below.

Enjoy

Nigel Moriarty

Articles

 CCTBX tools for derivative-free optimization

Short communications

 phenix.find_alt_orig_sym_mate

 Using force field generated models in the refinement of
crystallographic structures containing carbohydrates

 Viewing diffraction images in CCTBX

 On contribution of hydrogen atoms to X-ray scattering

--
Nigel W. Moriarty, Ph.D.

Coot, restraints and anchors

From: Morten Groftehauge
Date: 15 February 2012 12:16

Dear CCP4bb,

Is there any way to define a hydrogen bond as a restraint for real space refinement in Coot? It would be really useful for e.g. nucleotides where you might hypothesize or know that specific hydrogen bonds are formed.

Sincerely,

Morten

----------
From: Bernhard C. Lohkamp


You can try the scripts user-define-restraints.scm/user_defined_restraints.py which allow you to specify restraints. These are not available in the distribution (yet) but from google code:

http://code.google.com/p/coot/source/browse/trunk/scheme/user-define-restraints.scm
http://code.google.com/p/coot/source/browse/trunk/python/user_defined_restraints.py (*)

There is more on non-bonded restraints (including H-bonds) in the pipeline...

B

(*) just realised the name mismatch, so this may change at some point...

how to fix c-beta deviations

From: Anuradha Balasubramanian
Date: 15 February 2012 12:52

Dear all,

i am quite new to refinement and after refinement using refmac i have a resonable R-factor and R-free (22 and 27%), but Molprobity analysis shows c-beta devaition s as 23.

How can i fix this? 

--
B. Anuradha

Crystal Structures as Snapshots--Summary

From: Jacob Keller
Date: 15 February 2012 20:48

Dear Crystallographers,

thanks for all of the responses and conversation. I have culled
together the various references which have been sent on the BB and
which I have come up with, and posted them below. Worthy of special
mention, I think, is the first one (Lange et al), in which 46 (!)
different crystal structures are pitted against a lot of RDC NMR data,
and the match seems to be excellent (although it seems you probably
have to know both methods fairly well to evaluate this properly.)
Anyway, for asserting that variances between crystal structures at
least in some cases represent differences between
physiologically-relevant states in solution, the Lange paper is really
on the mark.

Thanks again,

Jacob

Lange OF, Lakomek NA, Farès C, Schröder GF, Walter KF, Becker S,
Meiler J, Grubmüller H, Griesinger C, de Groot BL.
Recognition dynamics up to microseconds revealed from an RDC-derived
ubiquitin ensemble in solution.
Science. 2008 Jun 13;320(5882):1471-5. PubMed PMID: 18556554.


Kondrashov, D.A., Zhang, W., Aranda, R.t., Stec, B., and Phillips,
G.N., Jr. (2008). Sampling of the native conformational ensemble of
myoglobin via structures in different crystalline environments.
Proteins 70, 353-362.

Zhang, X. J., Wozniak, J. A., and Matthews, B. W. (1995) Protein
flexibility and adaptability seen in 25 crystal forms of T4 lysozyme,
Journal of molecular biology 250, 527-552.

Long, SB, Casey, P., Beese, LS (2002) The reaction path of protein
farnesyltransferase at atomic resolution. Nature Oct 10;
419(6907):645-50.
http://www.ncbi.nlm.nih.gov/pubmed?term=The%20reaction%20path%20of%20protein%20farnesyltransferase%20at%20atomic%20resolution

J. R. Kiefer, C. Mao, J. C. Braman and L. S. Beese (1998) "Visualizing
DNA replication in a catalytically active Bacillus DNA polymerase
crystal" Nature 6664:304-7.
http://www.ncbi.nlm.nih.gov/pubmed?term=Visualizing%20DNA%20replication%20in%20a%20catalytically%20active%20Bacillus%20DNA%20polymerase%20crystal

Mancini EJ, Kainov DE, Grimes JM, Tuma R, Bamford DH, Stuart DI (2004)
"Atomic snapshots of an RNA packaging motor reveal conformational
changes linking ATP hydrolysis to RNA translocation."
Cell 118(6):743-55
http://www.cell.com/abstract/S0092-8674(04)00837-2

Nature. 2009 Dec 3;462(7273):669-73.
Hidden alternative structures of proline isomerase essential for catalysis.
Fraser JS, Clarkson MW, Degnan SC, Erion R, Kern D, Alber T.




*******************************************
Jacob Pearson Keller

----------
From: James Stroud


I feel compelled to throw a few references into the ring.


NFAT is a protein where you get a good sampling of snapshots:

1. Folded up as a monomer when interacting with partner proteins:

 http://www.ncbi.nlm.nih.gov/pubmed/9510247
 http://www.ncbi.nlm.nih.gov/pubmed/16873067

2. Extended as a dimer:

 http://www.ncbi.nlm.nih.gov/pubmed/12949493

3. Folded up as a monomer when interacting with a partner protein which happens to be itself as an extended dimer:

 http://www.ncbi.nlm.nih.gov/pubmed/18462673

4. Wrapped around DNA as a monomer without partners:.

 http://www.ncbi.nlm.nih.gov/pubmed/14643663


In this last reference you get a sample of extended, wrapped around, and folded up all in the same unit cell!


James