[ccp4bb] Reading LCF files.

[Jonathan Cooper]

For those who suffer from 80's nostalgia, I have worked-out a simple-man's way 
of recovering the reflection data from this, now obsolete, format. Its here:
https://readingccp4lcffiles.blogspot.com

and it works for most of my VAX lcf files. Just thought this might be of 
interest as the question has popped-up once or twice over the years!





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Re: [ccp4bb] HKL2000 - Error model

[Dominika Borek]

You should not adjust the error model manually, instead please select 
the button "use auto corrections" and rely on the automatically adjusted 
error model. This way you do not have to analyze the changes in the 
resolution shells.


D.


On 2019-07-01 01:44 PM, Weston Lane wrote:

When you fix the error model in HKL2000 you only have a set of
numbered boxes (1-20) and knowing which box corresponds to which
resolution bin and corresponding chi^2 value isn't apparent without
looking at the log file.

Besides using a script the easiest method IMO is graphically: hover
your mouse (with the red crosshairs) over the I/s and chi^2 vs
resolution plot @ the chi^2=1.0 hash mark and it's easy to see which
bin has the outlier values.  See the following screen grab for
clarity.  https://i.imgur.com/sr6JQy6.png

Wes



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--
Dominika Borek, Ph.D. *** UT Southwestern Medical Center
5323 Harry Hines Blvd. *** Dallas, TX 75390-8816
214-645-9577 (phone) *** 214-645-6353 (fax)



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Re: [ccp4bb] HKL2000 - Error model

[Weston Lane]

When you fix the error model in HKL2000 you only have a set of numbered boxes 
(1-20) and knowing which box corresponds to which resolution bin and 
corresponding chi^2 value isn't apparent without looking at the log file.

Besides using a script the easiest method IMO is graphically: hover your mouse 
(with the red crosshairs) over the I/s and chi^2 vs resolution plot @ the 
chi^2=1.0 hash mark and it's easy to see which bin has the outlier values.  See 
the following screen grab for clarity.  https://i.imgur.com/sr6JQy6.png

Wes



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Re: [ccp4bb] HKL2000 - Error model

[Eleanor Dodson]

What are we meant to make of that picture?
Eleanor

On Mon, 1 Jul 2019 at 18:39, De La Torre Marquez, Pedro L. <
delatorremarque...@osu.edu> wrote:

> Hi all,
>
> Highly recommended for people working with HKL2000. Please check the
> attached picture.
>
> By: Jesse Sandhu from Sotomayor Laboratory, The Ohio State University.
>
> 
>
> Best,
>
> Pedro.
>
>
>
>
>
>
> --
>
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>



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Re: [ccp4bb] inter- and atomic interactions comparison

[Jonathan Cooper]

For dynamics, you have probably already found VMD which is fairly easy to get 
started with.

Sent from Yahoo Mail on Android 
 
  On Mon, 1 Jul 2019 at 16:17, Mirella Vivoli Vega 
wrote:   Dear CCP Fo(r)lks,
I wonder if someone could help me about prediction servers or programs 
or molecular dynamics  I could use/run to compare the wild type protein 
structure and a mutant (I do not have the structure for the mutant), 
with/without substrate. The mutation (Asparagine to Aspartate) enhanced 
the hydrolysis of cellulosic substrates, increased the protein thermal 
stability, without affecting the protein fold. It would be interesting 
if there is a way to see the structural differences in the atomic and 
interatomic interactions determining the increased activity we have 
observed.
I really appreciate your comments, help and opinions.
Cheers,

Mirella


-- 
Mirella Vivoli Vega, PhD
Senior Postdoctoral Fellow
Department of Experimental and Clinical Biomedical Sciences,
University of Florence,Viale Morgagni 50, 50134, Florence, Italy
email: mirella.viv...@unifi.it

"I do not want to believe, I want to know"[c. Sagan]



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[ccp4bb] inter- and atomic interactions comparison

[Mirella Vivoli Vega]

Dear CCP Fo(r)lks,
I wonder if someone could help me about prediction servers or programs 
or molecular dynamics  I could use/run to compare the wild type protein 
structure and a mutant (I do not have the structure for the mutant), 
with/without substrate. The mutation (Asparagine to Aspartate) enhanced 
the hydrolysis of cellulosic substrates, increased the protein thermal 
stability, without affecting the protein fold. It would be interesting 
if there is a way to see the structural differences in the atomic and 
interatomic interactions determining the increased activity we have 
observed.

I really appreciate your comments, help and opinions.
Cheers,

Mirella


--
Mirella Vivoli Vega, PhD
Senior Postdoctoral Fellow
Department of Experimental and Clinical Biomedical Sciences,
University of Florence,Viale Morgagni 50, 50134, Florence, Italy
email: mirella.viv...@unifi.it

"I do not want to believe, I want to know"[c. Sagan]



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[ccp4bb] Mandatory PDBx/mmCIF format for crystallographic PDB depositions

[John Berrisford]

>From today, July 1st 2019, submission of PDBx/mmCIF format files for
crystallographic depositions to the PDB is mandatory.

Refmac, Phenix.refine, and Buster programs can now output PDBx/mmCIF
formatted files. For users of other structure determination/refinement
software packages, the wwPDB provides stand-alone and web-based tools to
convert legacy PDB format files into PDBx/mmCIF format: pdb_extract
  and MAXIT
 . More information on
outputting and preparing PDBx/mmCIF format files for deposition can be found
on the wwPDB website
 .

For more information, view the full news release at the wwPDB website
  or
contact the wwPDB on deposit-h...@mail.wwpdb.org
 .

 

Regards

 

John

 

--

John Berrisford

PDBe

European Bioinformatics Institute (EMBL-EBI)

European Molecular Biology Laboratory

Wellcome Trust Genome Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

  http://www.pdbe.org

 
http://www.facebook.com/proteindatabank

  http://twitter.com/PDBeurope

 




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Re: [ccp4bb] R values from an .mtz file containing Fobs and Fcalc

[Robbie Joosten]

But then you would loose the info on the solvent mask parameters. These are 
only implicitly stored in FC_ALL. These values too are things to get from 
data.json.

Cheers,
Robbie

On 1 Jul 2019 15:31, Eleanor Dodson  wrote:
Old program RSTATS would give r factor..

But easist to run 0 cycles of REFMAC - at least then you know what the scaling 
algorithm might be
Eleanor

On Mon, 1 Jul 2019 at 14:22, Robbie Joosten 
mailto:robbie_joos...@hotmail.com>> wrote:
If you are using SFTOOLS you might as well use the CORREL function to calculate 
things.

Datamining is easier though. Every PDB-REDO entry has a data.json file that has 
all the numbers you need.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board 
> [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Tim Grüne
> Sent: Monday, July 01, 2019 15:19
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] R values from an .mtz file containing Fobs and Fcalc
>
> Dear Andre,
>
> easiest would be to select the FP and FC_ALL with sftools, write out the
> values to a text file and calculate the R-value with a scripting language like
> awk.
>
> Best,
> Tim
>
> Am 01.07.2019 15:02, schrieb Andre LB Ambrosio:
> > Dear colleagues,
> >
> > Can a CCP4 program calculate r_work and r_free directly from a .mtz
> > file containing FP and FC_ALL (from PDB_REDO)? this without inputing
> > the matching .pdb file and ideally using a commando line.
> >
> > Many thanks in advance,
> >
> > --
> >
> > Andre LB Ambrosio
> >
> > -
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis Faculty of Chemistry
> University of Vienna
>
> Phone: +43-1-4277-70202
>
> GPG Key ID = A46BEE1A
>
> ##
> ##
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



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Re: [ccp4bb] post-doctoral position structural biology of ion channels

[chris . ulens]

A post-doctoral position is available at the Laboratory of Structural 
Neurobiology, KU Leuven Belgium (http://www.xtal.be ). The 
research in our laboratory is aimed at understanding the molecular mechanism of 
ligand-gated ion channels. Our method relies on X-ray crystallography and 
cryo-EM in combination with electrophysiological recordings and fluorescence 
spectroscopy. Our laboratory hosts an integrated macromolecular crystallization 
facility with a Mosquito crystallization robot and two RockImagers. Current 
structural targets include the family of pentameric ligand-gated ion channels 
(Cys-loop receptors), TRP channels and CNG channels.

We would like to recruit a post-doc with prior experience in expression, 
purification and crystallization of membrane proteins. Prior experience with 
X-ray crystallography or cryo-EM is considered a major advantage.

The successful candidate:
- easily communicates in an open verbal manner and has a team player spirit
- has an ambitious work ethic
- critically contributes to writing of manuscripts and grant proposals
- makes efforts to obtain independent funding
- meets intermediate deadlines and brings projects to a successful end
- fuels internal discussions of recent publications in the field
- sets an example to younger PhD students in the lab
- identifies directions for future scientific research

The position is open immediately and applications will be accepted until the 
position is filled. Applicants are requested to submit a CV with publication 
list and two references. E-mail to chris.ul...@kuleuven.be

Selected lab publications:

Molecular blueprint of allosteric binding sites in a homologue of the 
agonist-binding domain of the α7 nicotinic acetylcholine receptor. Spurny R, 
Debaveye S, Farinha A, Veys K, Vos AM, Gossas T, Atack J, Bertrand S, Bertrand 
D, Danielson UH, Tresadern G, Ulens C.
Proc Natl Acad Sci U S A. 2015 May 12;112(19):E2543-52.

Pentameric ligand-gated ion channel ELIC is activated by GABA and modulated by 
benzodiazepines. Spurny R, Ramerstorfer J, Price K, Brams M, Ernst M, Nury H, 
Verheij M, Legrand P, Bertrand D, Bertrand S, Dougherty DA, de Esch IJ, 
Corringer PJ, Sieghart W, Lummis SC, Ulens C. Proc Natl Acad Sci U S A. 2012 
Oct 30;109(44):E3028-34.

A structural and mutagenic blueprint for molecular recognition of strychnine 
and d-tubocurarine by different cys-loop receptors. Brams M, Pandya A, Kuzmin 
D, van Elk R, Krijnen L, Yakel JL, Tsetlin V, Smit AB, Ulens C.
PLoS Biol. 2011 Mar;9(3):e1001034.


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Re: [ccp4bb] R values from an .mtz file containing Fobs and Fcalc

[Andre LB Ambrosio]

Many thanks to all for the prompt and great inputs.
Best regards,
Andre.

Em seg, 1 de jul de 2019 às 10:32, Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> escreveu:

> Old program RSTATS would give r factor..
>
> But easist to run 0 cycles of REFMAC - at least then you know what the
> scaling algorithm might be
> Eleanor
>
> On Mon, 1 Jul 2019 at 14:22, Robbie Joosten 
> wrote:
>
>> If you are using SFTOOLS you might as well use the CORREL function to
>> calculate things.
>>
>> Datamining is easier though. Every PDB-REDO entry has a data.json file
>> that has all the numbers you need.
>>
>> Cheers,
>> Robbie
>>
>> > -Original Message-
>> > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
>> > Tim Grüne
>> > Sent: Monday, July 01, 2019 15:19
>> > To: CCP4BB@JISCMAIL.AC.UK
>> > Subject: Re: [ccp4bb] R values from an .mtz file containing Fobs and
>> Fcalc
>> >
>> > Dear Andre,
>> >
>> > easiest would be to select the FP and FC_ALL with sftools, write out the
>> > values to a text file and calculate the R-value with a scripting
>> language like
>> > awk.
>> >
>> > Best,
>> > Tim
>> >
>> > Am 01.07.2019 15:02, schrieb Andre LB Ambrosio:
>> > > Dear colleagues,
>> > >
>> > > Can a CCP4 program calculate r_work and r_free directly from a .mtz
>> > > file containing FP and FC_ALL (from PDB_REDO)? this without inputing
>> > > the matching .pdb file and ideally using a commando line.
>> > >
>> > > Many thanks in advance,
>> > >
>> > > --
>> > >
>> > > Andre LB Ambrosio
>> > >
>> > > -
>> > >
>> > > To unsubscribe from the CCP4BB list, click the following link:
>> > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>> >
>> > --
>> > --
>> > Tim Gruene
>> > Head of the Centre for X-ray Structure Analysis Faculty of Chemistry
>> > University of Vienna
>> >
>> > Phone: +43-1-4277-70202
>> >
>> > GPG Key ID = A46BEE1A
>> >
>> > ##
>> > ##
>> >
>> > To unsubscribe from the CCP4BB list, click the following link:
>> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>


-- 
Andre LB Ambrosio



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Re: [ccp4bb] R values from an .mtz file containing Fobs and Fcalc

[Eleanor Dodson]

Old program RSTATS would give r factor..

But easist to run 0 cycles of REFMAC - at least then you know what the
scaling algorithm might be
Eleanor

On Mon, 1 Jul 2019 at 14:22, Robbie Joosten 
wrote:

> If you are using SFTOOLS you might as well use the CORREL function to
> calculate things.
>
> Datamining is easier though. Every PDB-REDO entry has a data.json file
> that has all the numbers you need.
>
> Cheers,
> Robbie
>
> > -Original Message-
> > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> > Tim Grüne
> > Sent: Monday, July 01, 2019 15:19
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] R values from an .mtz file containing Fobs and
> Fcalc
> >
> > Dear Andre,
> >
> > easiest would be to select the FP and FC_ALL with sftools, write out the
> > values to a text file and calculate the R-value with a scripting
> language like
> > awk.
> >
> > Best,
> > Tim
> >
> > Am 01.07.2019 15:02, schrieb Andre LB Ambrosio:
> > > Dear colleagues,
> > >
> > > Can a CCP4 program calculate r_work and r_free directly from a .mtz
> > > file containing FP and FC_ALL (from PDB_REDO)? this without inputing
> > > the matching .pdb file and ideally using a commando line.
> > >
> > > Many thanks in advance,
> > >
> > > --
> > >
> > > Andre LB Ambrosio
> > >
> > > -
> > >
> > > To unsubscribe from the CCP4BB list, click the following link:
> > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> >
> > --
> > --
> > Tim Gruene
> > Head of the Centre for X-ray Structure Analysis Faculty of Chemistry
> > University of Vienna
> >
> > Phone: +43-1-4277-70202
> >
> > GPG Key ID = A46BEE1A
> >
> > ##
> > ##
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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>



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Re: [ccp4bb] R values from an .mtz file containing Fobs and Fcalc

[Robbie Joosten]

If you are using SFTOOLS you might as well use the CORREL function to calculate 
things. 

Datamining is easier though. Every PDB-REDO entry has a data.json file that has 
all the numbers you need.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Tim Grüne
> Sent: Monday, July 01, 2019 15:19
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] R values from an .mtz file containing Fobs and Fcalc
> 
> Dear Andre,
> 
> easiest would be to select the FP and FC_ALL with sftools, write out the
> values to a text file and calculate the R-value with a scripting language like
> awk.
> 
> Best,
> Tim
> 
> Am 01.07.2019 15:02, schrieb Andre LB Ambrosio:
> > Dear colleagues,
> >
> > Can a CCP4 program calculate r_work and r_free directly from a .mtz
> > file containing FP and FC_ALL (from PDB_REDO)? this without inputing
> > the matching .pdb file and ideally using a commando line.
> >
> > Many thanks in advance,
> >
> > --
> >
> > Andre LB Ambrosio
> >
> > -
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis Faculty of Chemistry
> University of Vienna
> 
> Phone: +43-1-4277-70202
> 
> GPG Key ID = A46BEE1A
> 
> ##
> ##
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



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Re: [ccp4bb] R values from an .mtz file containing Fobs and Fcalc

[Tim Grüne]

Dear Andre,

easiest would be to select the FP and FC_ALL with sftools, write out the 
values to a text file and calculate the R-value with a scripting 
language like awk.


Best,
Tim

Am 01.07.2019 15:02, schrieb Andre LB Ambrosio:

Dear colleagues,

Can a CCP4 program calculate r_work and r_free directly from a .mtz
file containing FP and FC_ALL (from PDB_REDO)? this without inputing
the matching .pdb file and ideally using a commando line.

Many thanks in advance,

--

Andre LB Ambrosio

-

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--
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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[ccp4bb] Error information during opening ccp4 in mac

[Zhang Foggy]

Dear all,

I got such kind of error information during opening ccp4 in mac. Can anyone
tell me how to fix it ? Thanks a lot!

Application initialization failed: couldn't connect to display
"/private/tmp/com.apple.launchd.hH7rs61iI7/org.macosforge.xquartz:0"

Error in startup script: can't read "tk_version": no such variable

while executing

"catch "set system(TK_VERSION) $tk_version""

(file "/Applications/ccp4-7.0/share/ccp4i/bin/ccp4i.tcl" line 1)

(file "/Applications/ccp4-7.0/bin/ccp4i" line 1)

Liang



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[ccp4bb] R values from an .mtz file containing Fobs and Fcalc

[Andre LB Ambrosio]

Dear colleagues,

Can a CCP4 program calculate r_work and r_free directly from a .mtz file
containing FP and FC_ALL (from PDB_REDO)? this without inputing the
matching .pdb file and ideally using a commando line.

Many thanks in advance,

-- 
Andre LB Ambrosio



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[ccp4bb] PhD student position at Umeå University

[Karina Persson]

Dear all,

A PhD position in biochemistry/structural biology is available at Umeå 
University, Sweden. The overall aim of the project is to obtain structural and 
functional data of bacterial fimbrial proteins and associated proteins involved 
in maturation of fimbria. Please forward to any suitable candidates.

The lab is part of the Integrated Structural Biology community at Umeå 
University, consisting of 14 research groups that use, and have access to, 
high-field NMR, X-ray crystallography, a world-class cryo-EM facility and 
computation biology with a high performance computing centre.


Full details are available at:
https://umu.mynetworkglobal.com/en/what:job/jobID:272296/

The closing date for applications is the 5th of Aug. 2019. Applications must be 
submitted online.

For more information regarding the research group:  
www.biostruct.umu.se/principal-investigators/karina-persson/

Please feel free to contact karina.pers...@umu.se if you have questions.

Best regards,

Karina Persson
Associate Professor
Department of Chemistry
Umeå University, Sweden




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[ccp4bb] Structural Biologist/biochemist position at Broad institute of MIT and Harvard

[ROPARS Virginie]

The Zhang Lab (zhanglab.bio) focuses on discovering and harnessing novel 
biological systems for development as molecular tools.  In addition to our work 
with CRISPR-Cas systems, we have recently identified a number of additional 
exciting biological systems and we are working to understand their function and 
mechanisms. We are looking to recruit a sharp, experienced, creative Structural 
Biologist to lead projects aimed at mechanistically characterizing these novel 
systems and rationally engineering them for use as biotechnologies.
The candidate will pursue his/her own structural biology projects within the 
group, collaborating with existing lab members or new hires as needed to 
advance the projects. Candidate must have strong background in biochemistry and 
structural biology research with successful demonstration of the ability to 
solve protein structures, and of particular interest, protein assemblies 
including RNA and DNA molecules. The ideal candidate will also possess superior 
experimental planning and execution skills, an open mind, curiosity about 
molecular mechanisms, and a strong desire to tinker.

The Zhang lab is a member of the Broad Institute of MIT and Harvard and 
McGovern Institute at MIT, and a part of the greater Boston life-science 
community including MIT and Harvard with ready access to structural biology 
resources, beamlines and Krios Cryo-TEM. Our lab is a fun, vibrant, fast-paced, 
result-driven, and collaborative environment with state-of-the-art research 
facilities and support from NIH, HHMI, and various foundations and 
philanthropies. We are a unique multidisciplinary lab working to bridge 
fundamental biology and development of biotechnology.

The Broad Institute of MIT and Harvard offers an outstanding place to work. The 
workplace culture is diverse, dynamic, progressive, and supports a healthy 
work-life balance. To support this mission, we strive for a workplace culture 
that supports diversity, intellectual curiosity, flexibility, and integrity. 
Broad employees receive a generous benefits package (including a highly 
competitive salary, dental, vision and health insurance, retirement plan, and 
additional benefits) and a range of possibilities for career advancement. 
Details on our benefits package can be found here - 
https://www.broadinstitute.org/benefits/benefits-working-broad


PRINCIPAL DUTIES AND RESPONSIBILITIES:

·   Develop, lead, and execute research projects

·   Stay current on the field and think deeply about creative new ways to 
have an impact

·   Contribute to the lab through teamwork and discussion

·   Help to train, supervise, and mentor junior staff as needed


MINIMUM QUALIFICATIONS:

·   PhD in relevant field (structural biology, biochemistry, biophysics, 
molecular biology)

·   Extensive experience with biochemical, structural, and/or biophysical 
experimental techniques

·   Demonstrated scientific contributions to the field

·   Proven ability to efficiently and effectively solve problems

Contact: zhangoff...@broadinstitute.org



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