[ccp4bb] Post-doc Position in time-resolved BioSAXS at the Max IV Laboratory

[Marjolein Thunnissen]

Hi

On behalf of my colleague Tómas Plivilic I would like to draw attention to a 
postdoctoral position within time_resolved BioSAXS opening at MAX IV in Lund, 
Sweden..


The CoSAXS beamline is a state-of-the-art multipurpose Small Angle X-ray 
Scattering (SAXS) instrument at MAX IV which is currently under construction 
(https://www.maxiv.lu.se/accelerators-beamlines/beamlines/cosaxs/). It will 
offer high brilliance, monochromatic and tunable X-rays, with outstanding 
performance in low beam divergence, high X-ray flux, and variable beam sizes in 
the full range of the sample-detector distances provided by the beamline (up to 
18 m).

The beamline will be equipped with state of the art SAXS/WAXS detectors. 
Several techniques will be available through modular operation: time resolved 
SAXS, SAXS/WAXS, protein solution SAXS (BioSAXS), micro-focusing SAXS and XPCS. 
It is due to commence full user operation in 2019.

We are offering a postdoctoral position to develop the capabilities of the 
beamline to perform time resolved BioSAXS measurements at seconds to 
milliseconds time scales. The postdoc should be prepared to integrate a flowing 
sample environment with rapid data collection strategies whilst, for example, 
inducing temperature jumps by either laser or terahertz radiation heating. 
Specific data interpretation strategies should be introduced.

The candidate will also be able to develop their own research projects 
exploring further possibilities for time resolved SAXS in a broader range of 
applications. Support will be provided including development beamtime and the 
possibility to apply for beamtime in other large scale facilities. The 
technical developments will be made available to the CoSAXS user community of 
MAX IV Laboratory. This position is funded through a Röntgen-Ångström-Cluster 
funded project “Non-equilibrium thermodynamics of biology studied by 
time-resolved small-angle X-ray and neutron scattering” (http://ttsas.eu).

For more information on this position see  
https://lu.varbi.com/en/what:job/jobID:184632/iframeEmbedded:0/where:4
To contact at Max IV: ann.te...@maxiv.lu.se or 
tomas.plivi...@maxiv.lu.se

Best regards

Marjolein Thunnissen
[cid:3A2194AC-734C-45EB-B5A7-CE7FC0F0F1BC]






Dr. Marjolein Thunnissen
Head User Office

MAX IV Laboratory
Lund University
P.O. Box 118, SE-221 00 Lund, Sweden
Visiting address: Fotongatan 2, 225 94 Lund
Telephone:+46 46 2224668
Mobile:  +46 766 32 04 17
www.maxliv.lu.se

Re: [ccp4bb] Help needed to make a clue about ligand

[Tristan Croll]

Looks like it could be a G-C dinucleotide?

 
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
 

 

> On 10 Jan 2018, at 04:09, Shankar Prasad Kanaujia  
> wrote:
> 
> Dear All,
> 
> Wishing you all a very happy and prosperous new year 2018
> 
> We have recently solved a structure which contains a huge density in the 
> active site. We modelled a molecule fitting the electron density (please see 
> the attached figures). However, we could not find any known molecule similar 
> to the fitted molecule either in PDB or PubChem databases. Thus, we are not 
> able to correlate its existence in cell.
> 
> The protein was expressed in E. coli cells. The structure is solved at 1.85 
> Angst. We have not added any molecule like this in any step of the 
> experiments.
> 
> Looking forward to having some ways to figure out this problem.
> 
> With best regards,
> Shankar
> 
> 
> -- 
> 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] PhD Positions, NIMHANS, Bangalore, India

[Padmanabhan B]

PhD Positions at NIMHANS, Bangalore, India

PhD positions are available in our Structural Biology lab. Our research work 
focus on drug discovery & development and understanding the molecular 
mechanisms of the protein targets associate with neurodegenerative diseases 
including Parkinson’s disease, ALS and glioma.

We are looking for the motivated candidates with graduation in Biophysics, 
Structural Biology, Protein Biochemistry, Biotechnology or related fields. The 
candidates also should have anyone of the qualifications such as CSIR-JRF/SRF, 
DBT-JRF/SRF, ICMR, or DST-Inspire.

The interested candidates may send their CV to balapa...@gmail.com or 
pa...@nimhans.ac.in


Best regards,
B. Padmanabhan



**
Dr. B. Padmanabhan, Ph. D
Professor & Head
Department of Biophysics
National Institute of Mental Health
and Neuro sciences (NIMHNAS)
Bangalore - 560029
India
Email: pa...@nimhans.ac.in;  balapa...@gmail.com

[ccp4bb] reindexing mtz

[Peter Hsu]

Dear all,

Looking to get some advice on reindexing an old dataset. I recently solved a 
structure of reasonable resolution at ~3A in C2. I had an old dataset at 4A in 
P213 that I never got a MR solution with until I solved the structure of it at 
3A. I've recently gone back to to this and managed to find a solution using 
MolRep. However, I've not been able to refine the solution to anything below an 
Rfree of 60. Went back to try it in P23 and also found solution, but was never 
able to refine it. 

I had a suggestion from my boss to reindex in a different space group (I23), 
but I've since misplaced the original image files (terrible) and only have the 
.X files from HKL. I'm wondering if it's possible to reindex using either CCP4 
or Phenix. I know there's a utility for it, but my understanding is poor and 
I'm not sure if I can go from P --> I using this program. 

Thanks for any input on this very dumb problem.

Peter

[ccp4bb] postdoctoral position - National Institutes of Health, Bethesda

[Antonina Roll-Mecak]

Please see below an opportunity for a postdoctoral fellowship in my lab at
the NIH. We are looking for enthusiastic, talented scientists who will
share our passion for microtubules and the beautiful world of tubulin
diversity.

Antonina


*Postdoctoral Fellowship *

*Cell Biology and Biophysics Unit, National Institutes of Health, Bethesda,
USA*

A postdoctoral fellowship opportunity is available in the Cell Biology and
Biophysics Unit headed by Dr. Antonina Roll-Mecak to work on structural and
functional studies of tubulin modification enzymes and molecular motors
using a combination of X-ray crystallography, cryo-EM and single molecule
fluorescence microscopy. Research in the Roll-Mecak lab focuses on
deciphering the tubulin code ie how tubulin posttranslational modifications
tune microtubule functions (see for instance Garnham et al., *Cell* 2015,
Valenstein et al., *Cell* 2016, Vemu et al., *JBC* 2016; Zehr et al *Nature
Struct & Molec Biology *2017).  For more information about the lab please
visit: https://neuroscience.nih.gov/ninds/rm_lab/

I am looking for enthusiastic, self-motivated Ph.D. graduates with a strong
publication record and expertise in molecular biology, biochemistry, X-ray
crystallography or electron microscopy who will welcome working in an
interdisciplinary group with a supportive atmosphere and excellent
resources. The Washingon DC area is a great place to live with great access
to cultural and outdoor activities. Experience with assembly of protein
complexes or structure determination by crystallographic methods or EM is a
must. The successful applicant will be awarded a NINDS Intramural
Fellowship.  Please send a CV, a one-page research experience summary and
contact information of three references to anton...@mail.nih.gov  Please
write “Fellow - tubulin code” in the subject header.


-- 


Antonina Roll-Mecak

Senior Investigator and Chief

Cell Biology and Biophysics Unit

Porter Neuroscience Research Center

NINDS and NHLBI

National Institutes of Health



Administrative contact: Karen Kendrick; Ph: 301-451-9223 <(301)%20451-9223>;
Email: karen.kendr...@nih.gov 

Lab website: https://neuroscience.nih.gov/ninds/RM_Lab/

[ccp4bb] post-doc position at SLAC/Stanford University

[van den Bedem, Henry]

Post-doctoral position in the Biosciences Division
at SLAC National Accelerator Laboratory/Stanford University

The Biosciences Division at SLAC National Accelerator Laboratory/Stanford 
University has an opening for a post-doctoral position. Our group works at the 
interface of computation and experiment to understand how proteins and ligands 
interact and function. For the successful candidate, there will be ample 
opportunity to get experience at the bench if desired.

Our research in computational structural biology and conformational dynamics 
centers on resolving spatiotemporally averaged data in ensemble experiments. 
Responsibilities for the position include developing novel computational, 
statistical and experimental methodologies to identify biomolecular ensembles 
and allosteric mechanisms from X-ray and electron sources, in close 
collaboration with the Fraser group at UCSF, leading academic groups at 
SLAC/Stanford, and our collaborators in the pharmaceutical industry. 
 
The position is for up to four years, and available immediately. Candidates 
must have a Ph.D. degree in a quantitative discipline, like computer science, 
applied mathematics, statistics, computational (bio)physics, or similar, and 
strong algorithm and software development skills (Python or C++). Demonstrated 
experience with X-ray crystallography/cryoEM data processing, or machine 
learning approaches would be a plus. 

SLAC National Accelerator Laboratory is a U.S. Department of Energy (DOE) 
Office of Science laboratory operated by Stanford University and has a unique 
set of large-scale facilities including the Linac Coherent Light Source (LCLS) 
X-ray Free-Electron Laser, the SLAC cryo-EM facilities, the Stanford 
Synchrotron Radiation Lightsource (SSRL), and state-of-the-art High-Performance 
Computing facilities. 

Come join us in sunny California!

Inquiries or applications, including a CV with publication list and two 
references to:
Henry van den Bedem (vdbe...@slac.stanford.edu)

[ccp4bb] CCP4MG error after installation

[Whitley, Matthew J]

Hello all,


After installing ccp4 7.0 and all updates via the package manager on CentOS 6, 
I receive the following error messages upon running ccp4mg:



libpng error: IDAT: invalid distance too far back
QPainter::begin: Paint device returned engine == 0, type: 2
QPainter::end: Painter not active, aborted


The path to the ccp4mg executable on our system is as follows:

/usr/local/ccp4-7.0/ccp4-7.0/bin/ccp4mg



I would appreciate any ideas about the source of the issue and how to resolve 
it.



Sincerely,

Matthew Whitley


---
Matthew J. Whitley, Ph.D.
Research Instructor
W. Furey Lab
Department of Pharmacology & Chemical Biology
University of Pittsburgh School of Medicine

Re: [ccp4bb] Super protein wire model bender

[David Schuller]

I think those used to be sold by the Charles Supper Co. Check out their 
cat# 7145


http://www.charles-supper.com/en/page/product.cfm?idProduct=33



On 01/09/18 03:34, syed ibrahim wrote:

Dear Friends

I am looking for the provider details of instrument - Byron Bender (or  super 
protein wire model bender), which is used to build protein wire model using 
Torsion angle for teaching purpose. I could not find any such provider.

I greatly appreciate your help

Thank you

Dr. B. Syed Ibrahim
Assistant Professor,
Centre for Bioinformatics
Pondicherry University
India - 605 008



--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

[ccp4bb] Phenix version 1.13 released

[Paul Adams]

The Phenix developers are pleased to announce that version 1.13 of Phenix is 
now available (build 1.13-2998). Binary installers for Linux, Mac OSX, and 
Windows platforms are available at the download site:

http://phenix-online.org/download/

Highlights for this version:

- phenix.map_to_model - better symmetry support and improved runtime efficiency 
- phenix.structure_search - structural library and internal support for mmCIF 
- phenix.ligand_identification - limit ligand size for search 
- Phaser 2.8.1 - various bug fixes 
- Structure Comparison - more/improved validation information (ligands, waters, 
cis/trans peptides, HIS protonation) 
- GUI - automatic validation after phenix.real_space_refine; visual 
improvements in validation
- Improved handling of model mmCIF input/output
- New Phenix video tutorials  
- Internal bug fixes and performance improvements

- NEW FEATURES

  - Phenix.map_to_model:
- Allows cases where symmetry that is neither point-group nor
   helical is present
- Allows splitting runs into many small independent steps
- Set defaults for quick=True to run somewhat more quickly

- GUI
  - Validation information added to phenix.real_space_refine results
  - phenix.real_space_refine GUI accepts input for reference models
  - Polygon stand-alone GUI deprecated; rolled into Comprehensive Validation GUI
- Old Polygon jobs cannot be restored
  - Validation GUI
- Stoplight colors (green/orange/red) added to validation summary
- In rotamer outlier table, uncalculated chi angles now display blank 
instead of None
- Validation table columns adjusted to reduce whitespace

- Updated dependencies
  - Python 2.7.13 -> 2.7.14
  - Boost 1.56 -> Boost 1.63
  - Numpy 1.8.1 -> 1.8.2

- phenix.structure_search:
  - Updated to November 2017 RCSB non-redundant library
(representatives of 100% sequence-identity clusters.)
  - Changed to mmcif-based coordinate handling internally.

- phenix.ligand_identification:
  - Added search limit on ligand sizes (Non-H atoms)
  - Run LigandFit algorithm internally as default.

- Phaser-2.8.1
  - bugfixes
- anisotropy correction of map coefficients after MR
- detection of duplicate solutions
- correct cell for PDB after refinement of cell for input data
- packing places molecules near origin in compact arrangement

- Structure Comparison
  - Updated to include favoured, allowed and outliers for validations tabs
such as rotamers
  - Add featurs such as ligands information & locations; water locations;
cis/trans peptides; and histidine protonation
  - General increase of robustness and flexibility
  - Greater flexibility for model/data input including directory tree travesal
and user defined scripts

- Restraints
  - Added better SF4 restraints
  - Added mechanism to improve SF4 linking

- Various performance enhancements

- Better handling of model mmCIF input/output

- New Phenix video tutorials:
  - Cryo-EM tools in Phenix - overview
  - How to run MolProbity - step by step (web interface and Phenix GUI)
  - MolProbity: All atom contacts tutorial

For a full list of changes see:

http://www.phenix-online.org/documentation/CHANGES

Please note that this publication should be used to cite use of Phenix:

PHENIX: a comprehensive Python-based system for macromolecular structure 
solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. 
Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. 
McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. 
Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010).

Full documentation is available here:

http://www.phenix-online.org/documentation/

There is a Phenix bulletin board:

http://www.phenix-online.org/mailman/listinfo/phenixbb/

Please consult the installer README file or online documentation for
installation instructions.

Direct questions and problem reports to the bulletin board or:

h...@phenix-online.org and b...@phenix-online.org

Commercial users interested in obtaining access to Phenix should visit the
Phenix website for information about the Phenix Industrial Consortium.

The development of Phenix is principally funded by the National Institute of
General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge
the generous support of the members of the Phenix Industrial Consortium.

-- 
Paul Adams
Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence 
Berkeley Lab
Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Laboratory Research Manager, ENIGMA Science Focus Area

Building 33, Room 347
Building 978, Room 4126
Tel: 1-510-486-4225, Fax: 1-510-486-5909
http://cci.lbl.gov/paul

Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 33R0345
Berkeley, CA 

Re: [ccp4bb] Na-Binding Protein?

[Diana Tomchick]

The human branched-chain alpha-ketoacid dehydrogenase requires a K+ ion to 
stabilize the binding of the cofactor thiamine diphosphate and to achieve 
maximum catalytic efficiency. See

https://www.ncbi.nlm.nih.gov/pubmed/10745006

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
University of Texas Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

On Jan 9, 2018, at 8:42 AM, Keller, Jacob 
mailto:kell...@janelia.hhmi.org>> wrote:

Dear Crystallographers,

Is anyone aware of a soluble protein which changes large-scale conformation +/- 
Na+, and is specific for Na+ per se, or at least ignores K+ and Ca++? E.g., Rb+ 
or Li+ might be okay. Structural info would be a plus, but not a sine qua non.

Similarly, what about with K+ or Cl- specificities, but oblivious to similar 
common ions?

All the best,

Jacob Keller

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
(571)209-4000 x3159
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.




UT Southwestern


Medical Center



The future of medicine, today.

Re: [ccp4bb] Na-Binding Protein?

[Patrick Shaw Stewart]

That's very interesting.  I guess it's an unusual manifestation of the
Hofmeister series.

It might give guidance to developers of screens for both crystallization
and cryoEM.

Thx, Patrick


On 9 January 2018 at 15:44, Andrew Mesecar  wrote:

> Dear Jacob,
>
>
>
> One of my favorite examples of monovalent cation discrimination is by the
> enzyme Pyruvate Kinase.  It prefers K(+), NH4(+), Rb(+) and Tl+ for maximum
> catalysis and then activity falls off as the monovalent cation sizes get
> larger, Cs(+) or smaller Na(+) >> Li (+).  The conformations of pyruvate
> kinase are known to be altered by binding of monovalent cations and it has
> been studied for over 50 years by a variety of approaches.  A number of the
> X-ray structures are with K(+).  I spent a few years of my life studying
> this enzyme a couple of decades ago.  It will hopefully provide some
> information for your project.
>
>
>
> Best of luck,
>
>
>
> Andy Mesecar
>
> On Tue, Jan 9, 2018 at 9:42 AM, Keller, Jacob 
> wrote:
>
>> Dear Crystallographers,
>>
>>
>>
>> Is anyone aware of a soluble protein which changes large-scale
>> conformation +/- Na+, and is specific for Na+ per se, or at least ignores
>> K+ and Ca++? E.g., Rb+ or Li+ might be okay. Structural info would be a
>> plus, but not a sine qua non.
>>
>>
>>
>> Similarly, what about with K+ or Cl- specificities, but oblivious to
>> similar common ions?
>>
>>
>>
>> All the best,
>>
>>
>>
>> Jacob Keller
>>
>>
>>
>> +
>>
>> Jacob Pearson Keller
>>
>> Research Scientist / Looger Lab
>>
>> HHMI Janelia Research Campus
>>
>> 19700 Helix Dr, Ashburn, VA 20147
>> 
>>
>> (571)209-4000 x3159 <(571)%20209-4000>
>>
>> +
>>
>>
>>
>> The content of this email is confidential and intended for the recipient
>> specified in message only. It is strictly forbidden to share any part of
>> this message with any third party, without a written consent of the sender.
>> If you received this message by mistake, please reply to this message and
>> follow with its deletion, so that we can ensure such a mistake does not
>> occur in the future.
>>
>>
>>
>
>
>
> --
> *Andrew D. Mesecar*
> Head, Department of Biochemistry
> Walther Professor of Cancer Structural Biology
> Deputy Director, Purdue Center for Cancer Research
> E-Mail: amese...@purdue.edu
> _
> *Department of Biochemistry Contact Information:*
> 175 S. University Street
> 
> W. Lafayette, IN 47907
> 
> -2063
> 765-494-1607
> --
> *Research Lab Contact Information:*
> Hockmeyer Hall of Structural Biology
> Room 311
> 
> 240 S. Martin Jischke Drive
> 
> West Lafayette, IN 47907
> 
> -1971
> 765-494-1924
> _
>
>



-- 
 patr...@douglas.co.ukDouglas Instruments Ltd.
 Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
 Directors: Peter Baldock, Patrick Shaw Stewart

 http://www.douglas.co.uk
 Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
 Regd. England 2177994, VAT Reg. GB 480 7371 36

Re: [ccp4bb] Na-Binding Protein?

[Bernhard Lechtenberg]

Dear Jacob,

The protease thrombin is another example. Thrombin is activated by Na+ (but not 
Li+ or K+). We have shown using NMR that Na+ binding allosterically stabilizes 
active conformations of thrombin. Additionally, numerous crystal structures of 
Na+-free (“slow” thrombin) and Na+-bound (“fast” thrombin) have been published.

These publications should give you a good overview:
https://www.ncbi.nlm.nih.gov/pubmed/20660315
https://www.ncbi.nlm.nih.gov/pubmed/22944689
http://www.pnas.org/content/100/24/13785/T1.expansion.html

Best,
Bernhard
Bernhard C. Lechtenberg, PhD
Postdoctoral Associate
Riedl Lab
Cancer Metabolism and Signaling Networks Program
NCI-Designated Cancer Center

[cid:24A04CE0-5418-4257-A8D1-8084CA766BC9@burnham.org]

10901 N. Torrey Pines Road, La Jolla, CA 92037
T  858.646.3100 ext. 4216  E 
blechtenb...@sbpdiscovery.org
Science Benefiting Patients®

On Jan 9, 2018, at 6:42 AM, Keller, Jacob 
mailto:kell...@janelia.hhmi.org>> wrote:

Dear Crystallographers,

Is anyone aware of a soluble protein which changes large-scale conformation +/- 
Na+, and is specific for Na+ per se, or at least ignores K+ and Ca++? E.g., Rb+ 
or Li+ might be okay. Structural info would be a plus, but not a sine qua non.

Similarly, what about with K+ or Cl- specificities, but oblivious to similar 
common ions?

All the best,

Jacob Keller

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
(571)209-4000 x3159
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

Re: [ccp4bb] Na-Binding Protein?

[Andrew Mesecar]

Dear Jacob,



One of my favorite examples of monovalent cation discrimination is by the
enzyme Pyruvate Kinase.  It prefers K(+), NH4(+), Rb(+) and Tl+ for maximum
catalysis and then activity falls off as the monovalent cation sizes get
larger, Cs(+) or smaller Na(+) >> Li (+).  The conformations of pyruvate
kinase are known to be altered by binding of monovalent cations and it has
been studied for over 50 years by a variety of approaches.  A number of the
X-ray structures are with K(+).  I spent a few years of my life studying
this enzyme a couple of decades ago.  It will hopefully provide some
information for your project.



Best of luck,



Andy Mesecar

On Tue, Jan 9, 2018 at 9:42 AM, Keller, Jacob 
wrote:

> Dear Crystallographers,
>
>
>
> Is anyone aware of a soluble protein which changes large-scale
> conformation +/- Na+, and is specific for Na+ per se, or at least ignores
> K+ and Ca++? E.g., Rb+ or Li+ might be okay. Structural info would be a
> plus, but not a sine qua non.
>
>
>
> Similarly, what about with K+ or Cl- specificities, but oblivious to
> similar common ions?
>
>
>
> All the best,
>
>
>
> Jacob Keller
>
>
>
> +
>
> Jacob Pearson Keller
>
> Research Scientist / Looger Lab
>
> HHMI Janelia Research Campus
>
> 19700 Helix Dr, Ashburn, VA 20147
> 
>
> (571)209-4000 x3159 <(571)%20209-4000>
>
> +
>
>
>
> The content of this email is confidential and intended for the recipient
> specified in message only. It is strictly forbidden to share any part of
> this message with any third party, without a written consent of the sender.
> If you received this message by mistake, please reply to this message and
> follow with its deletion, so that we can ensure such a mistake does not
> occur in the future.
>
>
>



-- 
*Andrew D. Mesecar*
Head, Department of Biochemistry
Walther Professor of Cancer Structural Biology
Deputy Director, Purdue Center for Cancer Research
E-Mail: amese...@purdue.edu
_
*Department of Biochemistry Contact Information:*
175 S. University Street
W. Lafayette, IN 47907-2063
765-494-1607
--
*Research Lab Contact Information:*
Hockmeyer Hall of Structural Biology
Room 311
240 S. Martin Jischke Drive
West Lafayette, IN 47907-1971
765-494-1924
_

Re: [ccp4bb] Na-Binding Protein?

[Conn Mallett]

Hi Jacob,

Ion-channel and receptor folks have been working on these types of 
questions... see: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2629458/


if you are looking for a model system, perhaps engineer a version of 
calmodulin that is specific for Na+ rather than Ca++?  Perhaps someone 
has already done that.


-Conn

Conn Mallett, PhD
Carlsbad, CA
conn.mallettgmail.com
skype: conn.mallett

On 9Jan2018 06:42, Keller, Jacob wrote:


Dear Crystallographers,

Is anyone aware of a soluble protein which changes large-scale 
conformation +/- Na+, and is specific for Na+ per se, or at least 
ignores K+ and Ca++? E.g., Rb+ or Li+ might be okay. Structural info 
would be a plus, but not a sine qua non.


Similarly, what about with K+ or Cl- specificities, but oblivious to 
similar common ions?


All the best,

Jacob Keller

+

Jacob Pearson Keller

Research Scientist / Looger Lab

HHMI Janelia Research Campus

19700 Helix Dr, Ashburn, VA 20147

(571)209-4000 x3159

+

The content of this email is confidential and intended for the 
recipient specified in message only. It is strictly forbidden to share 
any part of this message with any third party, without a written 
consent of the sender. If you received this message by mistake, please 
reply to this message and follow with its deletion, so that we can 
ensure such a mistake does not occur in the future.

[ccp4bb] Na-Binding Protein?

[Keller, Jacob]

Dear Crystallographers,

Is anyone aware of a soluble protein which changes large-scale conformation +/- 
Na+, and is specific for Na+ per se, or at least ignores K+ and Ca++? E.g., Rb+ 
or Li+ might be okay. Structural info would be a plus, but not a sine qua non.

Similarly, what about with K+ or Cl- specificities, but oblivious to similar 
common ions?

All the best,

Jacob Keller

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
(571)209-4000 x3159
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

[ccp4bb] proxy settings for ccp4 package manager

[Johannes Cramer]

Dear CCP4bb,

does anyone know how I can make the ccp4 package manager use a proxy for
downloading in Linux 64bit versions?
This would make installing and updating a whole lot easier for me...

I exported http_proxy, https_proxy, ftp_proxy (and all their capital letter
equivalents) and setup the system proxy in kde (although I think this only
matters for kde programs). I am using the 10.17 version of kubuntu, but
would also be interested in a solution that works for Mac.

Cheers,
Johannes

Re: [ccp4bb] Super protein wire model bender

[Conn Mallett]

You could possibly look up Byron Rubin directly, he will likely have 
some ideas He was in upstate NY last that I heard: 
https://rbj.net/2015/08/28/molecular-art/


Good luck!

-Conn

Conn Mallett, PhD
Carlsbad, CA
conn.mallettgmail.com
skype: conn.mallett

On 9Jan2018 02:57, mesters wrote:
Supper Protein Wire Model Bender Cat.#7145 



Not sure if they still make them.

- J. -


Am 09.01.18 um 09:34 schrieb syed ibrahim:

Dear Friends

I am looking for the provider details of instrument - Byron Bender (or  super 
protein wire model bender), which is used to build protein wire model using 
Torsion angle for teaching purpose. I could not find any such provider.

I greatly appreciate your help

Thank you

Dr. B. Syed Ibrahim
Assistant Professor,
Centre for Bioinformatics
Pondicherry University
India - 605 008



--
Dr.math. et dis. nat. Jeroen R. Mesters
Deputy, Senior Researcher & Lecturer
Program Coordinator /Infection Biology/ 



Institute of Biochemistry, University of Lübeck
Ratzeburger Allee 160, 23538 Lübeck, Germany
phone: +49-451-31013105 (secretariate -31013101)
fax: +49-451-31013104

http://jobs.zeit.de/image-upload/logo_10564.jpg
http://www.biochem.uni-luebeck.de 
http://www.eine-stadt-sieht-gelb.de 
http://www.uni-luebeck.de/studium/studiengaenge/infection-biology
http://www.iobcr.org 

Visiting Professorship in Biophysics, University of South Bohemia (CZ)
President of the International Organization for Biological 
Crystallization (IOBCr)

--
If you can look into the seeds of time and tell which grain will grow 
and which will not, speak then to me who neither beg nor fear 
(Shakespeare's Macbeth, Act I, Scene 3)

--
"Aujourd'hui je sais qu'il n'y a pas de limites à la bêtise humaine - 
qu'elle est infinie." (Gustave Flaubert, French novelist, 1821-1880)

--
It is invariably the case that high resolution X-ray structures show 
significantly better agreement with solution observables such as 
coupling constants, 13C chemical shifts, and proton chemical shifts, 
than the corresponding NMR structures, including the very best ones. 
Hence, in most cases, a high-resolution crystal structure (< 2.0 
Å)will provide a better description of the structure in solution than 
the corresponding NMR structure  (Kuszewski, Gronenborn & Clore, 1996, 
Protein Science 5:1067-80)

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[ccp4bb] Any issues using CCP4 under Mac OSX and High Sierra

[Jon R Sayers]

Are you Mac Users running CCP4 prods under High Sierra?
Sorry if I've missed this in an archive search but as a serial late adopter
of new OS releases, I've resisted upgrading until I know things work.

BW Jon

-- 
Professor Jon R Sayers, FRSB
Department of Infection, Immunity & Cardiovascular Disease
University of Sheffield Medical School
Beech Hill Rd
Sheffield
S10 2RX
United Kingdom

Tel: +44 (0)114 215 9552
Fax: +44 (0)114 271 1863
Email: j.r.say...@sheffield.ac.uk

http://www.sheffield.ac.uk/iicd/profiles/sayers

[ccp4bb] Diamond MX User Meeting at the CCP4 Study Weekend

[Ralf Flaig]

Dear All,

you can find the latest version of the Diamond MX User Meeting programme here:

https://eventbooking.stfc.ac.uk/meeting-info?meetingID=147

The meeting will be held Wednesday 10th January 2018 in the main lecture 
theatre at the EMCC.
Please note the earlier start time of 14:30h.

We hope to see you there.

Kind regards,
Pierre and Ralf



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retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

Re: [ccp4bb] Super protein wire model bender

[mesters]

Supper Protein Wire Model Bender Cat.#7145 



Not sure if they still make them.

- J. -


Am 09.01.18 um 09:34 schrieb syed ibrahim:

Dear Friends

I am looking for the provider details of instrument - Byron Bender (or  super 
protein wire model bender), which is used to build protein wire model using 
Torsion angle for teaching purpose. I could not find any such provider.

I greatly appreciate your help

Thank you

Dr. B. Syed Ibrahim
Assistant Professor,
Centre for Bioinformatics
Pondicherry University
India - 605 008



--
Dr.math. et dis. nat. Jeroen R. Mesters
Deputy, Senior Researcher & Lecturer
Program Coordinator /Infection Biology/ 



Institute of Biochemistry, University of Lübeck
Ratzeburger Allee 160, 23538 Lübeck, Germany
phone: +49-451-31013105 (secretariate -31013101)
fax: +49-451-31013104

http://jobs.zeit.de/image-upload/logo_10564.jpg
http://www.biochem.uni-luebeck.de 
http://www.eine-stadt-sieht-gelb.de 
http://www.uni-luebeck.de/studium/studiengaenge/infection-biology
http://www.iobcr.org 

Visiting Professorship in Biophysics, University of South Bohemia (CZ)
President of the International Organization for Biological 
Crystallization (IOBCr)

--
If you can look into the seeds of time and tell which grain will grow 
and which will not, speak then to me who neither beg nor fear 
(Shakespeare's Macbeth, Act I, Scene 3)

--
"Aujourd'hui je sais qu'il n'y a pas de limites à la bêtise humaine - 
qu'elle est infinie." (Gustave Flaubert, French novelist, 1821-1880)

--
It is invariably the case that high resolution X-ray structures show 
significantly better agreement with solution observables such as 
coupling constants, 13C chemical shifts, and proton chemical shifts, 
than the corresponding NMR structures, including the very best ones. 
Hence, in most cases, a high-resolution crystal structure (< 2.0 Å)will 
provide a better description of the structure in solution than the 
corresponding NMR structure  (Kuszewski, Gronenborn & Clore, 1996, 
Protein Science 5:1067-80)

--
Disclaimer
* This message contains confidential information and is intended only 
for the individual named. If you are not the named addressee you should 
not disseminate, distribute or copy this e-mail. Please notify the 
sender immediately by e-mail if you have received this e-mail by mistake 
and delete this e-mail from your system.
* E-mail transmission cannot be guaranteed to be secure or error-free as 
information could be intercepted, corrupted, lost, destroyed, arrive 
late or incomplete, or contain viruses. The sender therefore does not 
accept liability for any errors or omissions in the contents of this 
message, which arise as a result of e-mail transmission. If verification 
is required please request a hard-copy version. Please send us by fax 
any message containing deadlines as incoming e-mails are not screened 
for response deadlines.
* Employees of the Institute are expressly required not to make 
defamatory statements and not to infringe or authorize any infringement 
of copyright or any other legal right by email communications. Any such 
communication is contrary to Institute policy and outside the scope of 
the employment of the individual concerned. The Institute will not 
accept any liability in respect of such communication, and the employee 
responsible will be personally liable for any damages or other liability 
arising. Employees who receive such an email must notify their 
supervisor immediately.

--

[ccp4bb] study weekend live stream

[Charles Ballard]

Dear All

a little clunky, but here are the instructions.  Streaming starts for the 
what's new at 9am GMT tomorrow

Go to 
http://www.stfc.ac.uk/about-us/our-purpose-and-priorities/freedom-of-information/webinars/

And the select your device type.

 
 Charles

[ccp4bb] Super protein wire model bender

[syed ibrahim]

Dear Friends

I am looking for the provider details of instrument - Byron Bender (or  super 
protein wire model bender), which is used to build protein wire model using 
Torsion angle for teaching purpose. I could not find any such provider.

I greatly appreciate your help

Thank you

Dr. B. Syed Ibrahim
Assistant Professor,
Centre for Bioinformatics
Pondicherry University
India - 605 008