[ccp4bb] Postdoctoral position – Brohawn lab at the University of California, Berkeley

[Steve Brohawn]

The Brohawn lab at UC Berkeley, Department of Molecular and Cell Biology and 
Helen Wills Neuroscience Institute, seeks an outstanding postdoctoral scientist 
with a strong background in structural biology to join our team. 

We study cellular electrical excitability and sensory transduction through 
structural, mechanistic and physiological investigation of the ion channels, 
transporters and regulatory complexes that underlie these fundamental aspects 
of nervous system function. We use structural approaches (X-ray crystallography 
and cryo-electron microscopy) combined with electrophysiological, biophysical, 
and imaging techniques. For more information, please see the lab website 
(http://www.brohawnlab.org/) and some recent publications listed below.

The laboratory is well funded and equipped. Candidates will benefit from access 
to state of the art equipment and the exceptional community of structural 
biologists and neuroscientists at UC Berkeley and the surrounding San Francisco 
bay area. 

The position requires demonstrated experience in protein expression and 
purification and either X-ray crystallography or cryo-electron microscopy with 
a Ph.D. or M.D. in a related field. Experience in membrane protein 
biochemistry, cell culture and/or electrical recording is an asset, but is not 
required. Candidates motivated to learn biophysical and electrophysiological 
approaches to complement their structural background are encouraged to apply. 

Those interested should send a CV and contact information for three references 
to Prof. Stephen Brohawn: broh...@berkeley.edu


Brohawn, Campbell & MacKinnon, Nature 2014
Brohawn, Su & MacKinnon, PNAS 2014
Brohawn, Campbell & MacKinnon, PNAS 2013
Brohawn, del Mármol & MacKinnon, Science 2012
Brohawn, ANYAS 2015 (review) 

--
Stephen Brohawn, Ph.D.
Assistant Professor of Neurobiology
Department of Molecular and Cell Biology &
Helen Wills Neuroscience Institute
University of California, Berkeley

[ccp4bb] Job opportunities at Astex Pharmaceuticals, Cambridge UK

[Pamela Williams]

The Molecular Sciences Group at Astex Pharmaceuticals integrates multiple 
structural & biophysical techniques for fragment based drug discovery (FBDD). 
The group is currently expanding these approaches to include single particle 
cryo-EM. We are looking for a single particle cryo-EM scientist with experience 
in sample preparation and optimisation, data analysis, processing and 
reconstruction. 
 
In addition, we have an opening for a Bioformatics Scientist and are currently 
offering a number of Sustaining Innovation Fellowships.  

For full details of the vacancies and details on how to apply, please visit our 
job pages at http://www.astx.com/careers/ Closing date: 13th November, 2016.  

[ccp4bb] Instruct Biennial Structural Biology Meeting 2017

[Claudia Alen Amaro]

Dear All,

Instruct Biennial Structural Biology Registrations
open

The third Instruct Biennial Structural Biology
Meeting will take place in Brno, Czech Republic the
25-26^th of May 2017. Brno is the city of Johann
Gregor Mendel, a founder of modern genetics and one
of the first scientists who applied
multidisciplinary approach to explain his
observations. Social programme of the meeting will
include visit of the Mendel’s Museum and dinner at
the Augustinian Abbey, where Johann Gregor Mendel
worked and lived.

The inaugural Instruct Structural Biology Meeting at
Heidelberg in 2013 successfully showcased
integrative structural biology and its impact on
biological research and biomedicine. The second
Biennial took place in Florence in 2015 continuing
the integrative line with an increased focus on
innovation. This new edition will include sessions
that represent recent structural biology highlights,
emerging methods and technologies and results of
biomedical importance.

Confirmed speakers includes:

Speaker Name  Institute
Dave Stuart   Instruct/University of Oxford
Albert Heck   Utrecht University
Leemor Joshua-Tor Cold Spring Harbor Laboratory
Helen Saibil  Birkbeck College London
Masahide Kikkawa  University of Tokio
Juli Feigon   UCLA
Michael Sattler   TU Munich
Kristina  University of Vienna
Djinovic-Carugo
Babis Kalodimos   University of Minnesota
Richard Stefl Masaryk University
Janusz Brujnicki  International Institute of
  Molecular and Cell Biology
Andrew Carter MRC Laboratory of Molecular
  Biology, Cambridge
Thijn Brummelkamp Netherland Cancer Institute
James NaismithThe University St Andrews
Raymond Stevens   USC Dornsife
Petr Leiman   University of Texas Medical Branch

Upcoming submission opportunities/deadlines include:

Abstract submission: March 1

Registration closing: April 1

Student fellowships: March 1

We look forward to seeing you in Brno

The Instruct Operations Team

Dr Claudia Alen Amaro
Scientific Project Manager
Instruct: An Integrated Structural Biology
Infrastructure for Europe,
Wellcome Trust Centre for Human Genetics, University
of Oxford,
Roosevelt Drive, Headington OX3 7BN, UK
Tel: +44 1865 287808
email: clau...@strubi.ox.ac.uk
Follow us on twitter @instructhub

Re: [ccp4bb] Teaching models and cognition w/ xtallography as example, high school lvl

[Morten Grøftehauge]

Thanks for the help all,

I ended up using Protopedia for the list of Nobel Prizes but I really like
the Oxygen We Breathe tutorial and I've bookmarked it for future use.

In the end I had them read Ed Yong's article in The Atlantic about the
inevitable evolution of bad science. We talked about the transfer of models
(evolution model transferred from biology to social science) and the
problems and solutions for science listed in the article. I then used those
as a segue to talk about how one field, structural biology, actually had
already implemented several of those solutions and how successful the field
was, e.g. Nobel Prizes. The solutions were sharing models, sharing data,
cross-validation. And we also talked a bit about how there are too many
degrees of freedom compared to observations but we can add information
about order/connectivity of atoms, bond angles, bond lengths, etc. Even
something as simple as the rule that two atoms can't be on top of each
other is a lot of information.

Unfortunately, I ended up with too much information for 45 minutes. I could
have taken out the stuff about destructive and constructive interference
and why we chose x-ray over visible light without losing the points I
wanted to make. And I could have to sharpened up the lesson by spending
more time thinking about the take home message.

Cheers,
Morten


On 19 September 2016 at 15:09, Joel Sussman 
wrote:

>  19-Sep-2016
> Dear Morten
> Please consider looking at *Proteopedia*:  http://proteopedia.org, e.g.
> see:
> * 3D molecular models: an introduction 
> *http://www.proteopedia.org/w/3D_Molecular_Models
> *
> * HIV-1 *protease http://proteopedia.org/w/HIV-1_protease
> *
> * Group:SMART:A Physical Model of the β2-Adrenergic Receptor
> *http://www.proteopedia.org/w/Group:SMART:A_Physical_Model_of_the_%CE%B22-Adrenergic_Receptor
> *
> * Tutorial:How do we get the oxygen we breathe
> *http://proteopedia.org/w/Tutorial:How_do_we_get_the_oxygen_we_breathe
> *
> best regards,
> Joel
> 
> 
> Prof. Joel L. Sussman
> joel.suss...@weizmann.ac.il   *www.weizmann.ac.il/~joel
> *
> Dept. of Structural Biology   tel: +972  (8) 934 6309  
> *www.weizmann.ac.il/ISPC
> *
> Weizmann Institute of Science fax: +972  (8) 934 6312  *www.proteopedia.org
> *
> Rehovot 76100 ISRAEL  mob: +972 (50) 510 9600
> 
> -
>
> On 19Sep, 2016, at 13:53, Morten Grøftehauge <
> mortengroftehauge.w...@gmail.com >
> wrote:
>
> Hi everybody,
>
> I am teaching a single 45 minute lesson about models in natural science in
> a week long module on models and cognition. The students are in a science
> high school, age approx. 17. I thought xtallography would be a good example
> because it's very model-oriented, there's some stuff about validation and
> model precision indicators (e.g. r-values), models that build on other
> models (e.g. bond angles and lengths), data sharing vs not sharing etc.
> They can open PyMol and see some electron density, and I can automate a lot
> with scripts.
>
> Now I've googled a bit and looked at the teaching resources at RCSB PDB
> 101 but I can't seem to find anything that helps with what I want to show
> them. The guide to understanding PDB data looks like it has some useful
> things but it's very practically oriented (http://pdb101.rcsb.org/learn/
> guide-to-understanding-pdb-data/introduction). What I need to teach is
> more meta.
> *Does anyone know of any teaching resources that uses x-ray
> crystallography models as a basis for talking about scientific models in
> general?*
> If anyone has any great examples, specific structure-wise then please
> mention them. But I may just use some of my own as examples.
>
> Sincerely,
> Morten
>
>
>

[ccp4bb] Antw: Re: [ccp4bb] Antw: Re: [ccp4bb] High B factor

[Matthias Barone]

In my feeling, lowering the occ explains much more such unordered loops (or 
solvent exposed sidechains..). 
B-factors are a measure of uncertainty of the atom position xyz: Letting 
B-factors fly is like broadening a distribution to an extent where the 
expectation value looses its purpose. That in mind, I have no problem reducing 
the occ of a solvent-exposed lysine to 30% or even 10% if the atoms are not 
even visible in a FEM map...
best, matthias




>>> Tim Gruene  17.10.16 10.06 Uhr >>>
Dear Carlos and Phoebe,

the B-value describes the movement of an atom at first order approximation, 
i.e. as a harmonic motion. It's very unlikely that an atom that is not visible 
in density, discribes a harmonic motion. 
It never occurred to me, but modelling disorder by strong B-factor restraints 
and refining the occupancy seems quite a good idea and would be a much better 
model than an explosion of B-factors.
Coot marks atoms with reduced occupancy, hence there is no extra work required 
to visualise reduced occupancy. I am aware that some people use graphics 
rendering machinery to work with PDB files instead of a dedicated program like 
Coot, but you can never suit everyone.

Best,
Tim

On Monday, October 17, 2016 09:35:02 AM Carlos CONTRERAS-MARTEL wrote:
> Even that occupancy refinement seems to be very interesting for
> crystallographers, I complete agree with Phoebe.
> 
> On 10/14/16 17:38, Phoebe A. Rice wrote:
> > Interesting way to look at it.  But those loop residues are really in
> > the crystal with an occupancy of 1, so wouldn't letting the B factor
> > fly give a clearer description of what's in the crystal?  Especially
> > as many people know to color the structure by B factors to get a feel
> > for which bits are wiggly, but they'll never think to color it by
> > occupancy.
> 
> Let them fly ... at least for protein atoms ...
> 
> Carlos
> 
> > 
> > *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
> > Matthias Barone [bar...@fmp-berlin.de]
> > *Sent:* Friday, October 14, 2016 8:00 AM
> > *To:* CCP4BB@JISCMAIL.AC.UK
> > *Subject:* [ccp4bb] Antw: Re: [ccp4bb] High B factor
> > 
> > Picking up the mail of Pavel, Phenix refines occupancies..
> > If you expect the loops to be disordered, did you try to lower the
> > occupancy of these residues, following Ethan Merritt statement that
> > "general uncertainty [...] is represented better by occupancy <1
> > rather than an arbitrary large B factor" (To B or not to B,
> > doi:10.1107/S0907444911028320).
> > If this attempt does not bring the B-factors down, it will surely make
> > the model more accurate, as the atom coordinates of the loops may not
> > be correct at all, no?
> > 
> > matthias
> > 
> > >>> Pavel Afonine  14.10.16 9.36 Uhr >>>
> > >>> 
> > If you are still worry about your Bfactor, you could try TLS,
> > 
> > Or NCS, but SA with MLHL might be better.
> > 
> > (A joke).
> 
> --
>   Carlos CONTRERAS MARTEL, Ph.D.
>   (CR1 CNRS)
> 
>   carlos.contreras-mar...@ibs.fr
> 
>   "Bacterial Pathogenesis Group"
>  Institut de Biologie Structurale
>   UMR5075 CEA-CNRS-UGA
> 
>IBS
>Campus EPN
>71, avenue des Martyrs
>CS 10090
>38044 Grenoble CEDEX 9
>FRANCE
> 
> 
>   tel : (+33) (0)4 57 42 86 41
> 
> http://www.ibs.fr/groupes/groupe-pathogenie-bacterienne/?lang=fr
> http://www.ibs.fr/groups/bacterial-pathogenesis-group/?lang=en
-- 
--
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
Principal Investigator
Biology and Chemistry
OFLC/102
CH-5232 Villigen PSI

Phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A

Re: [ccp4bb] Antw: Re: [ccp4bb] High B factor

[Tim Gruene]

Dear Carlos and Phoebe,

the B-value describes the movement of an atom at first order approximation, 
i.e. as a harmonic motion. It's very unlikely that an atom that is not visible 
in density, discribes a harmonic motion. 
It never occurred to me, but modelling disorder by strong B-factor restraints 
and refining the occupancy seems quite a good idea and would be a much better 
model than an explosion of B-factors.
Coot marks atoms with reduced occupancy, hence there is no extra work required 
to visualise reduced occupancy. I am aware that some people use graphics 
rendering machinery to work with PDB files instead of a dedicated program like 
Coot, but you can never suit everyone.

Best,
Tim

On Monday, October 17, 2016 09:35:02 AM Carlos CONTRERAS-MARTEL wrote:
> Even that occupancy refinement seems to be very interesting for
> crystallographers, I complete agree with Phoebe.
> 
> On 10/14/16 17:38, Phoebe A. Rice wrote:
> > Interesting way to look at it.  But those loop residues are really in
> > the crystal with an occupancy of 1, so wouldn't letting the B factor
> > fly give a clearer description of what's in the crystal?  Especially
> > as many people know to color the structure by B factors to get a feel
> > for which bits are wiggly, but they'll never think to color it by
> > occupancy.
> 
> Let them fly ... at least for protein atoms ...
> 
> Carlos
> 
> > 
> > *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
> > Matthias Barone [bar...@fmp-berlin.de]
> > *Sent:* Friday, October 14, 2016 8:00 AM
> > *To:* CCP4BB@JISCMAIL.AC.UK
> > *Subject:* [ccp4bb] Antw: Re: [ccp4bb] High B factor
> > 
> > Picking up the mail of Pavel, Phenix refines occupancies..
> > If you expect the loops to be disordered, did you try to lower the
> > occupancy of these residues, following Ethan Merritt statement that
> > "general uncertainty [...] is represented better by occupancy <1
> > rather than an arbitrary large B factor" (To B or not to B,
> > doi:10.1107/S0907444911028320).
> > If this attempt does not bring the B-factors down, it will surely make
> > the model more accurate, as the atom coordinates of the loops may not
> > be correct at all, no?
> > 
> > matthias
> > 
> > >>> Pavel Afonine  14.10.16 9.36 Uhr >>>
> > >>> 
> > If you are still worry about your Bfactor, you could try TLS,
> > 
> > Or NCS, but SA with MLHL might be better.
> > 
> > (A joke).
> 
> --
>   Carlos CONTRERAS MARTEL, Ph.D.
>   (CR1 CNRS)
> 
>   carlos.contreras-mar...@ibs.fr
> 
>   "Bacterial Pathogenesis Group"
>  Institut de Biologie Structurale
>   UMR5075 CEA-CNRS-UGA
> 
>IBS
>Campus EPN
>71, avenue des Martyrs
>CS 10090
>38044 Grenoble CEDEX 9
>FRANCE
> 
> 
>   tel : (+33) (0)4 57 42 86 41
> 
> http://www.ibs.fr/groupes/groupe-pathogenie-bacterienne/?lang=fr
> http://www.ibs.fr/groups/bacterial-pathogenesis-group/?lang=en
-- 
--
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
Principal Investigator
Biology and Chemistry
OFLC/102
CH-5232 Villigen PSI

Phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A



signature.asc
Description: This is a digitally signed message part.

Re: [ccp4bb] Antw: Re: [ccp4bb] High B factor

[Carlos CONTRERAS-MARTEL]

Even that occupancy refinement seems to be very interesting for 
crystallographers, I complete agree with Phoebe.



On 10/14/16 17:38, Phoebe A. Rice wrote:
Interesting way to look at it.  But those loop residues are really in 
the crystal with an occupancy of 1, so wouldn't letting the B factor 
fly give a clearer description of what's in the crystal?  Especially 
as many people know to color the structure by B factors to get a feel 
for which bits are wiggly, but they'll never think to color it by 
occupancy.

Let them fly ... at least for protein atoms ...

Carlos




*From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of 
Matthias Barone [bar...@fmp-berlin.de]

*Sent:* Friday, October 14, 2016 8:00 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] Antw: Re: [ccp4bb] High B factor

Picking up the mail of Pavel, Phenix refines occupancies..
If you expect the loops to be disordered, did you try to lower the 
occupancy of these residues, following Ethan Merritt statement that 
"general uncertainty [...] is represented better by occupancy <1 
rather than an arbitrary large B factor" (To B or not to B, 
doi:10.1107/S0907444911028320).
If this attempt does not bring the B-factors down, it will surely make 
the model more accurate, as the atom coordinates of the loops may not 
be correct at all, no?


matthias


>>> Pavel Afonine  14.10.16 9.36 Uhr >>>

If you are still worry about your Bfactor, you could try TLS,


Or NCS, but SA with MLHL might be better.

(A joke).




--
 Carlos CONTRERAS MARTEL, Ph.D.
 (CR1 CNRS)

 carlos.contreras-mar...@ibs.fr

 "Bacterial Pathogenesis Group"
Institut de Biologie Structurale
 UMR5075 CEA-CNRS-UGA

  IBS
  Campus EPN
  71, avenue des Martyrs
  CS 10090
  38044 Grenoble CEDEX 9
  FRANCE


 tel : (+33) (0)4 57 42 86 41

http://www.ibs.fr/groupes/groupe-pathogenie-bacterienne/?lang=fr
http://www.ibs.fr/groups/bacterial-pathogenesis-group/?lang=en

Re: [ccp4bb] Structural biology software that does not run on Windows or gives important Windows-specific problems

[Mark J van Raaij]

Summary that I am going to use to justify buying MacOSX instead of Windows (in 
case this is of use to others):

Not available in Windows:
ADXV for looking at crystallographic diffraction images
XDS and HKL2000 for crystallographic data processing
(Auto)SHARP for phasing
ARPWARP for automated model building
(Auto)BUSTER for structure refinement
Uppsala Software Factory programs (Mapman, etc.), manipulation of maps and PDB 
files
Cryo-EM software (EMAN2, BSOFT)
 
Available in Windows but with important limitations:
Phenix (no MR-Rosetta, no parallelization)
DIALS (no parallelization)

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://wwwuser.cnb.csic.es/~mjvanraaij