[ccp4bb] Postdoctoral position in membrane protein structure and function at the NIH

[Anirban Banerjee]

There is an open postdoctoral position for a membrane protein
structure-function project in my lab at the NIH. We are currently focusing
on integral membrane enzymes (Science. 2018,  doi: 10.1126/science.aao6326)
and transporters of transition metal ions (J Biol Chem. 2018, doi:
10.1074/jbc.M117.817478).


Here is the formal announcement -

EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN
DEVELOPMENT, BETHESDA, MD AND SURROUNDING AREA

Position Description:
The research group of Dr. Anirban Banerjee at the National Institutes of
Health (NIH) is seeking candidates for postdoctoral fellows . The broad
interests of the lab are in membrane protein structure and function. We
combine structural techniques such as macromolecular crystallography with
biophysical and biochemical methods such as reconstitution based assays,
high resolution microscopy and small molecule screening to investigate the
structural bases of the mechanisms of a number of membrane proteins.

The lab has state-of-the-art equipment and facilities. We have dedicated
periodic access to the 22-ID beamline at the APS, for crystallographers at
the NIH, as well as access to 23-ID and 24-ID beam lines at the APS. Our
laboratory is part of the Cell Biology and Neurobiology Branch in the
Eunice Kennedy Shriver National Institute of Child Health and Human
Development (NICHD). We also have an affiliation to the National Institute
of Neurological Disorders and Stroke (NINDS).

Qualifications:
The candidates should hold a Ph. D. degree, be author of at least one first
author publication and have a strong background in biochemistry or
structural biology. Experience with basic molecular biology, protein
expression, purification and biochemical characterization are required.
Prior experience in membrane protein biochemistry or mammalian expression
system for protein purification will be added advantages.

It is absolutely essential the candidate is motivated and prepared to put
in the best efforts for fruition of the project goals. We are a small,
friendly lab and ability to work as part of a cohesive group is important.

To Apply:
Interested candidates can send an e-mail to anirban.baner...@nih.gov with a
CV and a summary of previous research experience and future interests.

The NIH is dedicated to building a diverse community in its training and
employment programs.

Re: [ccp4bb] Resolution cut off

[Vands]

Thanks, Robbie, I will try this.
-Vandna

On Mon, Feb 12, 2018 at 3:00 PM, Robbie Joosten 
wrote:

> Dear Vandna,
>
>
>
> Paired refinement is indeed the most reliable way to see whether the
> higher resolution data help your refinement. It is done automatically on
> the pdb-redo.eu server if the resolution of the data used in refinement
> so far is lower than the resolution of your dataset (by at least 0.1A). We
> get the resolution from your REMARK 3 stuff in the input pdb file header.
>
> Although it is not an ideal experiment, you can also cheat pdb-redo into
> doing paired refinement by forging the header of your pdb file.
>
>
>
> HTH,
>
> Robbie
>
>
>
> Sent from my Windows 10 phone
>
>
>
> *From: *Graeme Winter 
> *Sent: *maandag 12 februari 2018 20:48
> *To: *CCP4BB@JISCMAIL.AC.UK
> *Subject: *Re: [ccp4bb] Resolution cut off
>
>
>
> The most useful information for this can come from paired refinement,
> which will tell you if the data in outer shell is improving the model.
>
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689524/
>
> For example
>
> On balance it’s unlikely throwing away measurements will make your model
> better...
>
> Best wishes Graeme
> 
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Vands [
> vanx...@gmail.com]
> Sent: 12 February 2018 19:27
> To: ccp4bb
> Subject: [ccp4bb] Resolution cut off
>
> Hi,
>I solved a crystal structure at 1.69 A resolution with R /R free
> 18 / 20 i used 1.69 A data.
>
> Data completeness is 100 % and for the outer shell, it's 50 %. for i /Sig
> I > 1.
>
> Do I need to cut resolution in refinement??
>
> Vandna Kukshal
> Postdoctral Research Associate
> Dept. Biochemistry and Molecular Biophysics
> Washington University School of Medicine
> 660 S. Euclid
> , Campus
> Box 8231
> St. Louis, MO 63110
> --
> This e-mail and any attachments may contain confidential, copyright and or
> privileged material, and are for the use of the intended addressee only. If
> you are not the intended addressee or an authorised recipient of the
> addressee please notify us of receipt by returning the e-mail and do not
> use, copy, 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
>
>
>



-- 
Vandna Kukshal
Postdoctral Research Associate
Dept. Biochemistry and Molecular Biophysics
Washington University School of Medicine
660 S. Euclid, Campus Box 8231
St. Louis, MO 63110

Re: [ccp4bb] Resolution cut off

[Robbie Joosten]

Dear Vandna,

Paired refinement is indeed the most reliable way to see whether the higher 
resolution data help your refinement. It is done automatically on the 
pdb-redo.eu server if the resolution of the data used in refinement so far is 
lower than the resolution of your dataset (by at least 0.1A). We get the 
resolution from your REMARK 3 stuff in the input pdb file header.
Although it is not an ideal experiment, you can also cheat pdb-redo into doing 
paired refinement by forging the header of your pdb file.

HTH,
Robbie

Sent from my Windows 10 phone

From: Graeme Winter
Sent: maandag 12 februari 2018 20:48
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Resolution cut off

The most useful information for this can come from paired refinement, which 
will tell you if the data in outer shell is improving the model.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689524/

For example

On balance it’s unlikely throwing away measurements will make your model 
better...

Best wishes Graeme

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Vands 
[vanx...@gmail.com]
Sent: 12 February 2018 19:27
To: ccp4bb
Subject: [ccp4bb] Resolution cut off

Hi,
   I solved a crystal structure at 1.69 A resolution with R /R free  18 / 
20 i used 1.69 A data.

Data completeness is 100 % and for the outer shell, it's 50 %. for i /Sig I > 1.

Do I need to cut resolution in refinement??

Vandna Kukshal
Postdoctral Research Associate
Dept. Biochemistry and Molecular Biophysics
Washington University School of Medicine
660 S. Euclid, Campus Box 8231
St. Louis, MO 63110
--
This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
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] Resolution cut off

[Graeme Winter]

The most useful information for this can come from paired refinement, which 
will tell you if the data in outer shell is improving the model.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689524/

For example 

On balance it’s unlikely throwing away measurements will make your model 
better...

Best wishes Graeme 

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Vands 
[vanx...@gmail.com]
Sent: 12 February 2018 19:27
To: ccp4bb
Subject: [ccp4bb] Resolution cut off

Hi,
   I solved a crystal structure at 1.69 A resolution with R /R free  18 / 
20 i used 1.69 A data.

Data completeness is 100 % and for the outer shell, it's 50 %. for i /Sig I > 1.

Do I need to cut resolution in refinement??

Vandna Kukshal
Postdoctral Research Associate
Dept. Biochemistry and Molecular Biophysics
Washington University School of Medicine
660 S. Euclid, Campus Box 8231
St. Louis, MO 63110
-- 
This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
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

[ccp4bb] Resolution cut off

[Vands]

Hi,
   I solved a crystal structure at 1.69 A resolution with R /R free  18
/ 20 i used 1.69 A data.

Data completeness is 100 % and for the outer shell, it's 50 %. for i /Sig I
> 1.

Do I need to cut resolution in refinement??

Vandna Kukshal
Postdoctral Research Associate
Dept. Biochemistry and Molecular Biophysics
Washington University School of Medicine
660 S. Euclid, Campus Box 8231
St. Louis, MO 63110

Re: [ccp4bb] dials.image_viewer problem on Windows [CCP4 console]

[David Waterman]

Dear Rens de Vries,

Sorry for the trouble. Can you please try the following?

   1. Open the file C:\CCP4-7\7.0\InstallSetup.cmd in a text editor
   2. Change the string "--skip-phenix-dispatchers" to
   "--skip_phenix_dispatchers" (i.e. last two dashes to underscores)
   3. Save the file
   4. In a CCP4Console window cd to the directory C:\CCP4-7\7.0\
   5. Run the script InstallSetup.cmd by typing that name and pressing Enter
   6. Examine the log file called Installdisp.log (notepad.exe
Installdisp.log).
   You should see many lines with no errors, only some warnings.

Please let us know if this fixes the problem. We will release a fixed
installer soon.

-- David

On 12 February 2018 at 14:00, Vries, R.M.J.M. de 
wrote:

> Dear all,
>
>
>
> Although I normally use Linux for all my work with CCP4i2, I now use the
> Windows because of a workshop I will be giving. Here the audience is using
> Windows almost exclusively, therefore I chose to adapt to it.
>
>
>
> After using the xia2/DIALS pipeline I wanted to use the
> dials.reciprocal_lattice_viewer which, fortunately, worked absolutely
> fine (truly an amazing tool). I had to use the *CCP4 console *to make the
> dials-commands work. When I tried to apply the same method for the
> dials.image_viewer, it did not work. This is the console error message:
>
> https://pastebin.com/JNGRmu7G
>
>
>
> Which ends with:
>
> 1.  WindowsError: [Error 3] The system cannot find the path specified:
> 'c:\\ccp4-7\\7.0\\lib\\checkout\\cctbx-phaser\\cctbx_
> project\\rstbx\\slip_viewer/*.*'
>
> My slip_viewer is located in this directory by default:
>
> 'C:\CCP4-7\7.0\lib\py2\site-packages\cctbx_project\rstbx\slip_viewer'
>
>
>
> For me, the checkout folder in lib does not even exist. Any ideas to get
> around this problem?
>
>
>
> I am running CCP4i2 7.0.051 on Windows 7 (64 bit), but this error was also
> present on CCP4i2 7.0.051 on Windows 10 (64 bit).
>
>
>
> All the best,
>
>
>
> Rens de Vries
>
>
>

[ccp4bb] Tenure-Track Faculty Position in Structural Biology and Disease

[Matthew Neiditch]

Rutgers Biomedical and Health Sciences
 
Faculty Position in Structural Biology and Disease

The Department of Microbiology, Biochemistry, and Molecular Genetics and the 
interdepartmental Center for Immunity and Inflammation at Rutgers New Jersey 
Medical School seeks an exceptional Structural Biologist for a tenure-track 
faculty position at the level of Assistant Professor.  Rutgers New Jersey 
Medical School is located in Newark, NJ and is part of Rutgers Biomedical and 
Health Sciences (http://rbhs.rutgers.edu/), a division of Rutgers, The State 
University of New Jersey.

Applicants must have a Ph.D. and/or M.D. and at least 2 years of postdoctoral 
experience.  Candidates will be expected to establish a high-impact, funded 
independent research program that is focused on the prevention or cure of 
disease as well as participate in medical and graduate school education. A 
competitive start-up package will be provided. 

Information about the department may be found on our website at: 
http://njms.rutgers.edu/departments/molecular_genetics/index.cfm. 

For consideration, applicants should submit by email to 
mbmg-sea...@njms.rutgers.edu: a cover letter, curriculum vitae, a summary of 
past research accomplishments and future research plans and the names, 
affiliations and email addresses of 3-4 references.

You may also submit an application by regular mail to:

Dr. David Kaback, Chair of Faculty Search Committee
Department of Microbiology, Biochemistry and Molecular Genetics
New Jersey Medical School
Rutgers Biomedical and Health Sciences
225 Warren Street
Newark, NJ 07103

Rutgers University is an AA/EEO employer. All applicants will receive 
consideration for employment without regard to race, color, religion, sex, 
sexual orientation, gender identity, national origin, citizenship, disability 
or protected veteran status.

[ccp4bb] EM Validation Developer Post

[Maya Topf]

Dear all,


We are looking for a highly-motivated and creative Post Doctoral Researcher 
with a structural biology/bioinformatics background and experience in software 
development to work in Birkbeck College, London, on an exciting computational 
project in the field of cryoEM. The position is a part of a consortium funded 
by the Wellcome Trust to develop and disseminate validation tools to assess the 
quality of cryoEM reconstructions and fitted models.

Birkbeck is a wonderful place to work, with an exciting, international, 
collaborative environment that includes crystallographers, electron 
microscopists, bioinformatitions, and biochemists. 

The deadline is: 11 March 2018

More details can be found here: https://tinyurl.com/ya9b94cx


Many thanks and best wishes,

Maya Topf and Elena Orlova
Institute of Structural and Molecular Biology
Birkbeck College, University of London

[ccp4bb] dials.image_viewer problem on Windows [CCP4 console]

[Vries, R.M.J.M. de]

Dear all,

Although I normally use Linux for all my work with CCP4i2, I now use the 
Windows because of a workshop I will be giving. Here the audience is using 
Windows almost exclusively, therefore I chose to adapt to it.

After using the xia2/DIALS pipeline I wanted to use the 
dials.reciprocal_lattice_viewer which, fortunately, worked absolutely fine 
(truly an amazing tool). I had to use the CCP4 console to make the 
dials-commands work. When I tried to apply the same method for the 
dials.image_viewer, it did not work. This is the console error message:
https://pastebin.com/JNGRmu7G

Which ends with:
1.  WindowsError: [Error 3] The system cannot find the path specified: 
'c:\\ccp4-7\\7.0\\lib\\checkout\\cctbx-phaser\\cctbx_project\\rstbx\\slip_viewer/*.*'
My slip_viewer is located in this directory by default:
'C:\CCP4-7\7.0\lib\py2\site-packages\cctbx_project\rstbx\slip_viewer'

For me, the checkout folder in lib does not even exist. Any ideas to get around 
this problem?

I am running CCP4i2 7.0.051 on Windows 7 (64 bit), but this error was also 
present on CCP4i2 7.0.051 on Windows 10 (64 bit).

All the best,

Rens de Vries