[ccp4bb] PhD position in Structural Biology in Norway

[Hans-Petter Hersleth]

Dear all,
 
A 3- or 4-year PhD position in Structural Biology / Biophysics / Biochemistry 
starting August 2015 is available at University of Oslo, Department of 
Biosciences, Section for Biochemistry and Molecular Biology in the 
Metalloprotein group.
 
The project is in the field of structural biology, biophysics and biochemistry 
with an emphasis on protein crystallography and spectroscopy (UV-vis, Raman and 
EPR) in combination with other biochemical and biophysical methods.

The project is dealing with different redox proteins involved in oxygen 
activation and electron transfer. The focus will be on some enzyme systems like 
ribonucleotide reductase and nitric oxide synthase, their reaction mechanism 
and redox activation pathways.  
 
More information about the project, position and application procedure is found 
on the website:
http://uio.easycruit.com/vacancy/1352831/96323?iso=no
 
Applicants must hold a Master's degree or equivalent in structural biology, 
bioinorganic chemistry, biochemistry, biophysics, protein crystallography or 
related fields.

We are seeking a highly motivated candidate that should have skills and 
experience in working with proteins or bioinorganic molecules. It would be 
advantageous with hands-on experience within topics like cloning, protein 
expression, purification, crystallisation, protein crystallography, 
spectroscopy, bioinorganic chemistry, protein-protein interactions, enzyme 
kinetics and redox-, radical- and metalloproteins. 
 
Candiates without a Master's Degree have until 30 June 2015 to complete the 
final exam.
 
Application deadline is 13th April 2015 through the website: 
http://uio.easycruit.com/vacancy/1352831/96323?iso=no
 
For further information please contact: Dr. Hans-Petter Hersleth, 
(h.p.hersl...@ibv.uio.no)
 

--
Hans-Petter Hersleth, PhD
Project Leader, Researcher and Senior Lecturer
Department of Biosciences, University of Oslo
Section for Biochemistry and Molecular Biology
P.O.Box 1066 Blindern, NO-0316 Oslo, Norway
http://www.mn.uio.no/ibv/personer/vit/hphersle/index.html
---

Re: [ccp4bb] Offtopic: Software to closely visualize interacting partnets in protein complex

[Debasish Kumar Ghosh]

Thank you all for your valuable suggestions. They have really worked well for 
me :)

Regards,

Debasish Kumar Ghosh

CSIR- Junior Research Fellow (PhD Scholar)
C/o: Dr. Akash Ranjan
Computational and Functional Genomics Group
Centre for DNA Fingerprinting and Diagnostics
Hyderabad, INDIA

Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com
Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab)
Lab URL: http://www.cdfd.org.in/labpages/computational_functional_genomics.html

[ccp4bb] Vacancy for a Scientific Programmer Bioimaging & EMPIAR at PDBe

[Gerard DVD Kleywegt]

Hi all,

We are looking to recruit an experienced and motivated "Scientific Programmer 
Bioimaging & EMPIAR" to join the Protein Data Bank in Europe (PDBe) team at 
the European Bioinformatics Institute (EBI) located on the Wellcome Trust 
Genome Campus near Cambridge in the UK.


PDBe has recently launched EMPIAR (http://pdbe.org/empiar), an archive of raw 
2D image data from electron microscopy and electron tomography experiments. We 
now plan to extend and improve the archival, integration and dissemination of 
cellular imaging data from a range of other modalities including 3D scanning 
electron microscopy (3D-SEM), soft X-ray tomography (SXT) and correlative 
light and electron microscopy (CLEM). We are therefore seeking to recruit an 
enthusiastic scientific programmer with outstanding programming skills to join 
the EMPIAR development team.


For more information, see:

 https://ig14.i-grasp.com/fe/tpl_embl01.asp?newms=jj&id=53570&aid=15470

For informal enquiries, please contact Ardan Patwardhan , who 
is in charge of the EMPIAR project.


Best wishes,

--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] Graphics cards for Coot, Pymol, Chimera on MacBook Pro Laptop

[Marc Graille]

Hello,

I would like to buy a MacBook Pro laptop that will allow me among others to 
solve structures, build models and visualize electron density maps using Pymol, 
Coot or Chimera.
I have the choice between between Intel Iris Pro (5200 series) and Intel Iris 
Pro + Nvidia GT 750M for the graphics cards but I don’t know which one is fine 
for the programs I want to run.
Can some of you share advices/feedback with me?

Thanks a lot for your answer.

Best wishes,

Marc


Dr Marc GRAILLE

Directeur de recherche CNRS

Team: Translation and degradation of eukaryotic mRNAs

Team supported by the ATIP-Avenir CNRS program

Laboratoire de Biochimie

ECOLE POLYTECHNIQUE - UMR7654 CNRS

91128 PALAISEAU CEDEX


Phone : +33 (0)1 69 33 48 90 – Fax : +33 (0)1 69 33 49 09


Office 033012B

Email: marc.grai...@polytechnique.edu

http://bioc.polytechnique.fr/spip.php?rubrique117

 
 

[ccp4bb] Fwd: Structure with high B-factor

[Manish Shah]

Hi All,

I solved a structure using molecular replacement (Phaser) and the current
R-factor and R-free is 0.2 and 0.25. The electron density looks great for
residues and the ligand, however, the issue is with the B-values. The
average B-value is 110 at this stage of refinement and I could not bring it
down. All the residues are having a high B-values ranging from 90-120,
while the R is good. I have tried several options in CCP4 (restrained
refinement in Refmac) to bring it down and also used other MR programs, but
still it still continues to be in the same range.

I will look forward to any suggestions. Thank you.

Re: [ccp4bb] Fwd: Structure with high B-factor

[Ethan A Merritt]

On Tuesday, 17 March, 2015 17:34:24 Manish Shah wrote:
> Hi All,
> 
> I solved a structure using molecular replacement (Phaser) and the current
> R-factor and R-free is 0.2 and 0.25. The electron density looks great for
> residues and the ligand, however, the issue is with the B-values. The
> average B-value is 110 at this stage of refinement and I could not bring it
> down. All the residues are having a high B-values ranging from 90-120,
> while the R is good. I have tried several options in CCP4 (restrained
> refinement in Refmac) to bring it down and also used other MR programs, but
> still it still continues to be in the same range.
> 
> I will look forward to any suggestions. Thank you.

What was the Wilson B factor reported by Aimless or Truncate?
What is the resolution of the data?

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

[ccp4bb] OS X yosemite

[Cygler, Miroslaw]

Hi,
I am thinking of upgrading the os on my mac to Yosemite. Are there any known 
issues for crystallographic software that I should pay attention to?
Thanks,

Mirek

Re: [ccp4bb] Graphics cards for Coot, Pymol, Chimera on MacBook Pro Laptop

[Mark Brooks]

Hi Marc,
  I have an Intel Iris Pro graphics chip on a Late 2013 MacBook 
Pro which works impressively well with all these programs, even on a 15 inch 
Retina display. I don’t know if the Nvidia one is better though...

Bonne chance,

Mark

> On 17 Mar 2015, at 16:12, Marc Graille  wrote:
> 
> Hello,
> 
> I would like to buy a MacBook Pro laptop that will allow me among others to 
> solve structures, build models and visualize electron density maps using 
> Pymol, Coot or Chimera.
> I have the choice between between Intel Iris Pro (5200 series) and Intel Iris 
> Pro + Nvidia GT 750M for the graphics cards but I don’t know which one is 
> fine for the programs I want to run.
> Can some of you share advices/feedback with me?
> 
> Thanks a lot for your answer.
> 
> Best wishes,
> 
> Marc
> 
> 
> 
> Dr Marc GRAILLE
> 
> Directeur de recherche CNRS
> 
> Team: Translation and degradation of eukaryotic mRNAs
> 
> Team supported by the ATIP-Avenir CNRS program
> 
> Laboratoire de Biochimie
> 
> ECOLE POLYTECHNIQUE - UMR7654 CNRS
> 
> 91128 PALAISEAU CEDEX
> 
> 
> Phone : +33 (0)1 69 33 48 90 – Fax : +33 (0)1 69 33 49 09
> 
> 
> Office 033012B
> 
> Email: marc.grai...@polytechnique.edu 
> http://bioc.polytechnique.fr/spip.php?rubrique117 
> 
> 
>  
>  
> 

Re: [ccp4bb] OS X yosemite

[William G. Scott]

Hi Mirek:

I haven’t encountered anything (CCP4, phenix, coot. pymol, etc) that doesn’t 
work, but also haven’t found a single compelling advantage (or even a 
non-compelling advantage) to upgrading.

You get to see more of the spinning beachball of death while waiting for file 
dialog boxes to materialize.

YMMV,

Bill

William G. Scott
Professor, Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
University of California at Santa Cruz
Santa Cruz, California 95064  
USA

http://scottlab.ucsc.edu/~wgscott

> On Mar 17, 2015, at 4:30 PM, Cygler, Miroslaw  
> wrote:
> 
> Hi,
> I am thinking of upgrading the os on my mac to Yosemite. Are there any known 
> issues for crystallographic software that I should pay attention to?
> Thanks,
> 
> 
> Mirek
> 
> 
> 

Re: [ccp4bb] OS X yosemite

[Anindito Sen]

HI Mirek,

You may wanna to check for codes using  libpng12.0.dylib. 

This you have to get from other sources.

Best 

Andy 



Anindito Sen. Ph.D
Scientist & Application Specialist in Biological Sciences
JEOL LTD.
13F, Ohtemachi Nomura Bldg 
2-1-1 Ohtemachi Chiyoda-Ku. Tokyo, Japan
Tel: +81-3-6262-3563
Fax: +81-3-6262-3577

www.jeol.com




> On Mar 18, 2015, at 11:57 AM, William G. Scott  wrote:
> 
> Hi Mirek:
> 
> I haven’t encountered anything (CCP4, phenix, coot. pymol, etc) that doesn’t 
> work, but also haven’t found a single compelling advantage (or even a 
> non-compelling advantage) to upgrading.
> 
> You get to see more of the spinning beachball of death while waiting for file 
> dialog boxes to materialize.
> 
> YMMV,
> 
> Bill
> 
> William G. Scott
> Professor, Department of Chemistry and Biochemistry
> and The Center for the Molecular Biology of RNA
> University of California at Santa Cruz
> Santa Cruz, California 95064  
> USA
> 
> http://scottlab.ucsc.edu/~wgscott
> 
>> On Mar 17, 2015, at 4:30 PM, Cygler, Miroslaw  
>> wrote:
>> 
>> Hi,
>> I am thinking of upgrading the os on my mac to Yosemite. Are there any known 
>> issues for crystallographic software that I should pay attention to?
>> Thanks,
>> 
>> 
>> Mirek
>> 
>> 
>> 

Re: [ccp4bb] Graphics cards for Coot, Pymol, Chimera on MacBook Pro Laptop

[mesters]

Hello Marc,

obvious differences between card are memory bandwidth, intel 13 GB/sec 
vs. nvidia 29 GB/s, the texture rate, 2 GTexel/s vs. 31 GTexel/s, and 
pixel rate,  0.5 GPix/s vs. 15.5 GPix/s. Some of these values result 
because of graphics memory differences. There is no difference in energy 
consumption. Question is indeed, what do you need for doing 
crystallography. If you look at the performance in popular games, the 
difference is much less than you would expect looking only at the naked 
values. The intel is merely 20% slower than the nvidia in most reference 
games So, not worth spending the extra money I would say as the 
actual graphics performance between cards is similar.


However, if you plan to process a lot of graphical data (video editing, 
etc), the nvidia will by far out-perform the intel. Otherwise, the Intel 
Iris Pro model is more than fine and you better invest your money by 
getting more memory.


Best wishes

Jeroen


On 17 Mar 2015, at 16:12, Marc Graille > wrote:


Hello,

I would like to buy a MacBook Pro laptop that will allow me among others 
to solve structures, build models and visualize electron density maps 
using Pymol, Coot or Chimera.
I have the choice between between Intel Iris Pro (5200 series) and 
Intel Iris Pro + Nvidia GT 750M for the graphics cards but I don’t know 
which one is fine for the programs I want to run.

Can some of you share advices/feedback with me?

Thanks a lot for your answer.

Best wishes,

Marc


--
Dr.math. et dis. nat. Jeroen R. Mesters
Deputy, Senior Researcher & Lecturer
Coordinator master's program Infection Biology

Institute of Biochemistry, University of Lübeck
Ratzeburger Allee 160, 23538 Lübeck, Germany
phone: +49-451-5004065 (secretariate -5004061)
fax: +49-451-5004068

http://www.biochem.uni-luebeck.de 
http://www.uni-luebeck.de/studium/studiengaenge/infection-biology
http://www.iobcr.org 


--
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)

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