[ccp4bb] Postdoctoral Fellow Position in Structural Bioinformatics at RCSB PDB/UC San Diego

[Rose, Peter]

Summary: We are looking for a talented and highly motivated postdoc to join our 
multidisciplinary team at UC San Diego.

The Challenge: Develop innovate analysis, data integration, query, and 
visualization tools for 3D biomolecular structures to help accelerate research 
and training in biology, medicine, and related disciplines. In this project, we 
will employ the latest advances in computer science to develop highly 
interactive features and scalable services and workflows for the RCSB PDB 
website (http://www.rcsb.org).

This position is a unique opportunity to engage in leading edge research, 
development, and outreach activities of the RCSB PDB with worldwide impact.

Qualifications: Ph.D. in one or more of the following research areas

·   Structural Bioinformatics, or related field with a focus on software 
development

·   Structural Biology with a focus on software development

·   Computer Science with a focus on bioinformatics algorithm development 
or visualization

Demonstrated proficiency in a high-level programming language, such as Java or 
Python and experience with state of the art software development tools. 
Experience with front-end programming languages (JavaScript) and libraries. 
Strong skills in problem solving and algorithm design are required. High 
productivity demonstrated by publications and contributions to open source 
software projects. Experience in the development of modern web applications, 
user interface design, or scientific visualization is a plus. Excellent written 
and oral communication skills.

Note, this position is reviewed annually on the basis of performance and can be 
renewed.

Our Environment:

The Structural Bioinformatics Group 
(http://bioinformatics.sdsc.edu) at the San 
Diego Supercomputer Center (SDSC) (http://www.sdsc.edu) 
is involved in research and development activities centered around 3D 
structures of proteins and nucleic acids, the integration of structural data 
with other domains such as Medicine, Genomics, Biology, Drug Discovery, and the 
development of scalable solution to Big Data problems in Structural 
Bioinformatics. Our group leads the RCSB Protein Data Bank (PDB) west-coast 
operations. The RCSB PDB (http://www.rcsb.org) represents 
the preeminent source of experimentally determined macromolecular structure 
information for research and teaching in biology, biological chemistry, and 
medicine. With over 300,000 unique users from over 160 countries around the 
world, the RCSB PDB is one of the leading worldwide Biological Databases. Our 
group is also involved in the National Institutes of Health (NIH) Big Data to 
Knowledge (BD2K) initiative.

As an Organized Research Unit of UC San Diego, SDSC is a world leader in 
data-intensive computing and cyber infrastructure, providing resources, 
services, and expertise to the national research community, including industry 
and academia.

To apply, please send cover letter and resume to Dr. Peter Rose 
(peter.r...@rcsb.org).

--
Peter Rose, Ph.D.
Site Head, RCSB Protein Data Bank West 
(http://www.rcsb.org)
Principal Investigator, Structural Bioinformatics Laboratory 
(http://bioinformatics.sdsc.edu)
San Diego Supercomputer Center (http://www.sdsc.edu)
University of California, San Diego
+1-858-822-5497

Re: [ccp4bb] Crystals grow at the bottom of the tube.

[Artem Evdokimov]

Hi Lingyuan,

1) you're very lucky (but you already know that)
2) crystals grown quickly in bulk rarely diffract well. I would follow up
by a conventional droplet crystallization against a concentrating agent -
in the cold - such that your protein gradually concentrates from [X] to 2-3
times [X] and that should presumably give you crystals. Another option is
temperature-driven crystallization (if this is what is happening) in which
case a simple setup consists of a sitting or hanging drop plate inside a
closed styrofoam box that you set up at room temperature, then bring the
box (already closed) into a cold room - the box adds a considerable delay
factor. If you want to extend the cooling process even more you could place
a few Blue Ice packs in the box (again, at room temperature).

Artem

www.harkerbio.com
"protein crystals for breakfast, lunch, AND dinner"


- Cosmic Cats approve of this message

On Tue, Oct 18, 2016 at 6:41 AM, kiki  wrote:

> Dear all users,
>
>  I got my crystals at the bottom of the tube on ice just before I started
> to screen crystals. Those crystals' shapes were good but easy to melt when
> I harvested them. I shot these crystals. They only diffracted to 7A to 8A.
> Has anyone ever met this situation before? How to improve?
>
> Thanks,
> Lingyuan
>

Re: [ccp4bb] Wilson B-factors recorded for all PDB's to 3.5Å

[sunanda williams]

Polygon in the validation tools of phenix.


On Saturday, October 15, 2016, amit sharma <
0d1d6aa5c57b-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi,
>
> What is the average Wilson B-factor for all single crystal protein
> structures deposited in PDB at 3.5Å? Is there any software or a publication
> which could provide such an estimate?
>
> Thanks,
>
> Amit
>

[ccp4bb] Postdoctoral position in serial crystallography at the Paul Scherrer Institute

[Joerg Standfuss]

My group at the PSI is looking for a postdoctoral fellow to join our
efforts to establish injector based serial crystallography for the Swiss
Free Electron Laser. For this you produce, optimize & characterize crystals
of the target proteins. You will participate in the biophysical
characterization using synchrotron radiation sources and at X-ray Free
Electron Lasers (XFELs).

The position is part of the PSI-FELLOW-II-3i program by which the PSI
invites postdocs from all over the world to submit their applications. The
postdoctoral program offers unique opportunities for scientific and career
development with international and interdisciplinary prospects as part of
the Horizon2020 Marie Skłodowska-Curie COFUND Action.

More information under: https://www.psi.ch/pa/job-opportunities/1391
or by mail to: joerg.standf...@psi.ch

Best Regards,
Joerg

__
Dr. Jörg Standfuss
Serial Femtosecond Crystallography
Paul Scherrer Institute
CH-5232 Villigen PSI
http://www.psi.ch/lbr/standfuss_-joerg

Re: [ccp4bb] Wilson B-factors recorded for all PDB's to 3.5Å

[Pavel Afonine]

Hi Amit,

you will find the answer on page 47 here:
https://www.phenix-online.org/presentations/latest/pavel_validation.pdf

Pavel

On Sat, Oct 15, 2016 at 7:38 AM, amit sharma <
0d1d6aa5c57b-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi,
>
> What is the average Wilson B-factor for all single crystal protein
> structures deposited in PDB at 3.5Å? Is there any software or a publication
> which could provide such an estimate?
>
> Thanks,
>
> Amit
>

[ccp4bb] Crystals grow at the bottom of the tube.

[kiki]

Dear all users,


 I got my crystals at the bottom of the tube on ice just before I started to 
screen crystals. Those crystals' shapes were good but easy to melt when I 
harvested them. I shot these crystals. They only diffracted to 7A to 8A. Has 
anyone ever met this situation before? How to improve?


Thanks,
Lingyuan

[ccp4bb] SFB-AFC/GTBIO meeting: Extension of abstract submission deadline

[alberto podjarny]

Registration is now open for the joint SFB-AFC/GTBIO meeting (French
Biophysical Society –Special Interest Group Biology of the French
Crystallographic Association) to be held from December 13 to December 16
2016 at the VVF center, Obernai, France.


For the scientific program, abstract submissions & registration see
 http://sfb-gtbio2016.u-strasbg.fr/index.php
 The abstract submission deadline is November 1, 2016.


The registration deadline is November 15, 2016.

-- 
Alberto D. Podjarny
Directeur de Recherche CNRS
IGBMC
1, rue Laurent Fries
67404 Illkirch
TE: (33) 3 69 48 52 89
FAX: (33) 3 88 65 32 01
Mobile: (33) 6 11 65 31 92

 Please send mail to apodja...@gmail.com *

[ccp4bb] One postdoctoral fellow position is available immediately for cryo-EM single particle analysis of membrane proteins at Paul Scherrer Institut (PSI), Villigen Switzerland

[Xiaodan Li]

A postdoctoral fellow position is available immediately at the Paul Scherrer 
Institute in the group of Dr. Xiaodan Li at the Laboratory of Biomolecular 
Research (https://www.psi.ch/lbr/li_-xiaodan). The group has track record on 
structure determination of membrane protein using 2D and 3D crystals and is 
currently expanding the structure determination using to single particle 
cryo-EM. We are looking for a single particle cryo-EM postdoctoral research 
with experience in sample preparation and optimization, data analysis, 
processing and reconstruction. Previous experience working with membrane 
proteins will be an advantage but not a prerequisite. 

The Laboratory of Biomolecular Research at PSI has all facilities and 
instruments for protein expression, purification, biochemical and biophysical 
analysis (https://www.psi.ch/lbr/laboratory-of-biomolecular-research), as well 
as the full access to the PSI crystallization facility and the Swiss Light 
Source synchrotron radiation facility 
(https://www.psi.ch/sls/pxiii/crystallisation-facility). The group benefits 
from the in-house 200 kV screening transmission electron microscope (JEOL 
JEM2200). Furthermore, the group has access to the center for cellular imaging 
and nano analytics (C-CINA) in the University of Basel including the K2 and 
Falcon II direct detector-equipped Titan Krios microscope for high-resolution 
imaging and Polara (300kV) with K2 and MediPix Direct electron detector for 
electron nanocrystallography (https://c-cina.unibas.ch/).

Interested candidates could send an e-mail to xiao...@psi.ch for informal 
inquires.  The application should include a cover letter describing the 
candidate`s research interests and motivation to apply, the CV and list of 
publications, and contact details of three referees.