Re: [ccp4bb] Turning off the bulk solvent modelling in Refmac5 to generate Polder maps?

[Holton, James M]

Yes, Dorothee is right.  Don't turn off all the bulk solvent!  That is not a 
polder map.

In refmac you want to use the keyword:
solvent exclude DUM

And then fill the space you want to have no bulk solvent with water atoms with 
residue ID "DUM" and perhaps occupancy set to zero, since you don't want them 
contributing to Fcalc.  You might also want to turn off clashes for these dummy 
atoms using:
vdwrestraints DUMM 0
or
vdwrestraints exlcude

documentation is here:
https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html

Refmac also supports externally-defined solvent, which can be very handy.  All 
you need is structure factors (amplitudes and phases) in the same MTZ file as 
your data.  I like to call them Fsolvent PHIsolvent. Put these on the LABIN 
line with FPART1=Fsolvent PHIP1=PHIsolvent.  You will probably also want to use:
SCPART 1
Tells refmac to optimize the scale and B factor assigned to your bulk solvent.
You probably also want:
SOLVNET NO
This turns off the built-in bulk solvent calculation.  If you don't do this, 
refmac will scale its own default bulk solvent mask alongside your 
manually-provided mask.  Then again, you might want to do that just to see what 
happens.  In fact, you can provide refmac with several "partial structure" 
masks.  All of them will get scaled if you put their number on the SCPART line.

If you want the map that refmac uses by default, use the MSKOUT feature to have 
refmac write it out for you.  You can then scale this map with mapmask to make 
sure it has a range from 0 to 1.  You might also want to use other map masking 
tools on it.  Once you have a solvent map you want to use, you can convert this 
map into structure factors using refmac's "mode sfcalc" feature.  Also 
documented on the link above.  Then you can provide them as FPART1 PHIP1 as 
above.

-James Holton
MAD Scientist

On 2/4/2019 4:13 PM, Dorothee Liebschner wrote:
Hi,

Please note that for polder maps, the bulk solvent is reset locally. Turning 
bulk solvent off entirely most likely deteriorates maps.

Best wishes,

Dorothee

On Mon, Feb 4, 2019 at 3:50 AM Samuel Davis (PG Research) 
mailto:s.w.da...@dundee.ac.uk>> wrote:
Hi,

I'm wondering if anyone knows if it is possible to turn off the bulk solvent 
modelling in Refmac5, for the purpose of generating Polder maps? I know that an 
option for Polder maps is directly implemented in Phenix, but we ideally want 
to use Refmac5, as we have used it for the rest of our refinement and want to 
keep it consistent if possible.

Thanks,

Samuel.

Samuel Davis
MRC 3.5 Year Programme PhD Student
Life Sciences, Biological Chemistry and Drug Discovery, University of Dundee
+44 (0)1382 388325 | swda...@dundee.ac.uk

Scottish University of the Year
The Times / Sunday Times Good University Guide 2016 and 2017

Follow my blog: https://musingsofanearlycareerscientist.wordpress.com

The University of Dundee is a registered Scottish Charity, No: SC015096



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--
Project Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org



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[ccp4bb] Multiple Postdoctoral Fellowships available at the “Multiscale Research Institute for Complex Systems” at Fudan University of Shanghai

[Guo Lingyue]

 
Dear All, The Multiscale Research Institute for Complex Systems (MRICS) at Fudan University is located at the Zhangjiang Campus of Fudan University and is supported by the Shanghai High-level Talents Program. MRICS is strongly committed to the development of novel and effective multi-scale imaging technology that spans microscopic molecular structures all the way to macroscopic medical imaging, with the aim to provide unprecedented spatial and temporal insights into the structures and functions of living beings at all levels (molecules, cells, tissues, organs and even whole organisms). Specifically for structural biology, MRICS is equipped with a state-of-the-art cryo-EM facility that includes FEI Titan Krios equipped with Volta phase plate, Glacios, Talos and Aquilos. MRICS is also located next to Shanghai Synchrotron Radiation Facility for X-ray crystallography. Our team includes Nobel laureate and international leading interdisciplinary experts. We have new openings for multiple postdoctoral fellows in structural biology who will be mainly involved in structural studies of important biological systems by means of X-ray crystallography and cryo-electron microscopy including single-particle and tomography.Requirements:  The applicants should have a recent Ph.D. degree (within three years of graduation) or will have a Ph.D. degree within the next six months in biology or chemistry-related fields, are devoted to excellence in scientific research, have strong sense of responsibility, and are highly motivated and hardworking.  For these positions, extensive experience in protein _expression_ and purification is a must, while prior experience in X-ray crystallography or cryo-EM is a plus, but is not required.   Compensation:  1)   We offer internationally competitive salary and fringe benefits, the level of salary will be determined according to the applicant's experience and qualification; 2)   We will assist in applying for low-rent housing in Shanghai and provide certain housing subsidies; 3)   We have ample opportunities to collaborate with renown laboratories worldwide; 4)   We provide support for applying for funding opportunities whenever applicable.   Shanghai is one of the most international metropolitan cities in China with strong economy and vibrant scientific community.  For interested applicants, please submit postdoctoral application packages (a combined pdf) including resumes, concise research interest statements, representative publications, phone numbers and email addresses of three academic referees to:  Miss Guo (Email: ly...@fudan.edu.cn).  We look forward to your joining of our first-class team!Lingyue GUOThe Multiscale Research Institute for Complex SystemsFudan UniversityShanghai, China



 




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Re: [ccp4bb] Turning off the bulk solvent modelling in Refmac5 to generate Polder maps?

[Eleanor Dodson]

The keywords are:

SCALE TYPE SIMPLE
SOLVENT NO

I always use for a completed sctructure
SCALE TYPE SIMPLE
SOLVENT YES
and then a set of 4 numbers for scale and Bfactors are output .

There is an option to give these as a FIXED SCALE.

Forgotten the exact keywords but they will be in the manual..
Probably that is the best procedure for each POLDER map?

Eleanor

Maybe t

On Tue, 5 Feb 2019 at 00:13, Dorothee Liebschner 
wrote:

> Hi,
>
> Please note that for polder maps, the bulk solvent is reset locally.
> Turning bulk solvent off entirely most likely deteriorates maps.
>
> Best wishes,
>
> Dorothee
>
> On Mon, Feb 4, 2019 at 3:50 AM Samuel Davis (PG Research) <
> s.w.da...@dundee.ac.uk> wrote:
>
>> Hi,
>>
>> I'm wondering if anyone knows if it is possible to turn off the bulk
>> solvent modelling in Refmac5, for the purpose of generating Polder maps? I
>> know that an option for Polder maps is directly implemented in Phenix, but
>> we ideally want to use Refmac5, as we have used it for the rest of our
>> refinement and want to keep it consistent if possible.
>>
>> Thanks,
>>
>> Samuel.
>>
>> Samuel Davis
>> MRC 3.5 Year Programme PhD Student
>> Life Sciences, Biological Chemistry and Drug Discovery, University of
>> Dundee
>> +44 (0)1382 388325 | swda...@dundee.ac.uk
>>
>> Scottish University of the Year
>> The Times / Sunday Times Good University Guide 2016 and 2017
>>
>> Follow my blog: https://musingsofanearlycareerscientist.wordpress.com
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>
>
> --
> Project Scientist, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> 1 Cyclotron Road, M/S 33R0345
> Berkeley, CA 94720
> Tel: (510) 486-5709
> Fax: (510) 486-5909
> Web: https://phenix-online.org
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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>



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Re: [ccp4bb] Turning off the bulk solvent modelling in Refmac5 to generate Polder maps?

[Dorothee Liebschner]

Hi,

Please note that for polder maps, the bulk solvent is reset locally.
Turning bulk solvent off entirely most likely deteriorates maps.

Best wishes,

Dorothee

On Mon, Feb 4, 2019 at 3:50 AM Samuel Davis (PG Research) <
s.w.da...@dundee.ac.uk> wrote:

> Hi,
>
> I'm wondering if anyone knows if it is possible to turn off the bulk
> solvent modelling in Refmac5, for the purpose of generating Polder maps? I
> know that an option for Polder maps is directly implemented in Phenix, but
> we ideally want to use Refmac5, as we have used it for the rest of our
> refinement and want to keep it consistent if possible.
>
> Thanks,
>
> Samuel.
>
> Samuel Davis
> MRC 3.5 Year Programme PhD Student
> Life Sciences, Biological Chemistry and Drug Discovery, University of
> Dundee
> +44 (0)1382 388325 | swda...@dundee.ac.uk
>
> Scottish University of the Year
> The Times / Sunday Times Good University Guide 2016 and 2017
>
> Follow my blog: https://musingsofanearlycareerscientist.wordpress.com
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>


-- 
Project Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org



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Re: [ccp4bb] Turning off the bulk solvent modelling in Refmac5 to generate Polder maps?

[Edwin Pozharski]

It should be according to the manual

http://www.ccp4.ac.uk/html/refmac5/keywords/xray-principal.html#solv

If you using CCP4i, I believe this is done by unchecking the "Calculate the
contribution from the solvent region" box in Scaling section.

---
I don't know why the sacrifice didn't work. The science seemed so solid.
Julien XIII, Lord of the Lemurs

On Mon, Feb 4, 2019 at 6:50 AM Samuel Davis (PG Research) <
s.w.da...@dundee.ac.uk> wrote:

> Hi,
>
> I'm wondering if anyone knows if it is possible to turn off the bulk
> solvent modelling in Refmac5, for the purpose of generating Polder maps? I
> know that an option for Polder maps is directly implemented in Phenix, but
> we ideally want to use Refmac5, as we have used it for the rest of our
> refinement and want to keep it consistent if possible.
>
> Thanks,
>
> Samuel.
>
> Samuel Davis
> MRC 3.5 Year Programme PhD Student
> Life Sciences, Biological Chemistry and Drug Discovery, University of
> Dundee
> +44 (0)1382 388325 | swda...@dundee.ac.uk
>
> Scottish University of the Year
> The Times / Sunday Times Good University Guide 2016 and 2017
>
> Follow my blog: https://musingsofanearlycareerscientist.wordpress.com
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
> --
>
> 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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[ccp4bb] refmac same residue different names

[Edwin Pozharski]

Belated happy 2019, everyone.

For whatever obscure reason, I need to refine a model that has two
different residue types as alternate conformers with the same residue ID.
Presented with a pdb file that has such feature, Refmac fails saying this

 ERROR: in chain A residue: 443
> different residues have the same number
>
> There is an error in the input coordinate file
> At least one the chains has 2 residues with the same number
> Check above to see error
> ===> Error: Problem with coordinate file


There are several ways of getting around this I can think of.  Perhaps
duplicate chain with strict NCS for all but the residue in question could
work.  Perhaps adding this residue as two separate chains and then adding
enough LINK records to keep things in place could.  Either solution here is
inelegant and requires reformating pdb file back to sanity prior to
deposition.

Is there some way to allow different geometries for alternate conformers
that is native to Refmac?

Cheers,

Ed.

PS.  I know that phenix.refine takes the mixed name pdb file straight up.
I still want to be able to refine such structure with refmac (and buster,
actually, but that's a question I already asked in the appropriate forum.


Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
-- / Lao Tse /



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[ccp4bb] Structural biology and assay development/biophysics positions available at ICR, London, UK

[Rob Van Montfort]

The Institute of Cancer Research, London, is one of the world’s most 
influential cancer research institutes, with an outstanding record of 
achievement dating back more than 100 years. We provided the first convincing 
evidence that DNA damage is the basic cause of cancer, laying the foundation 
for the now universally accepted idea that cancer is a genetic disease. Today, 
The Institute of Cancer Research (ICR) leads the world at isolating 
cancer-related genes and discovering new targeted drugs for personalised cancer 
treatment.

The Cancer Research UK Cancer Therapeutics Unit (CTU), within the Division of 
Cancer Therapeutics, is a multidisciplinary 'bench to bedside' centre, 
comprising around 160 staff dedicated to the discovery and development of novel 
therapeutics for the treatment of cancer. The CTU’s exciting goal is to 
discover high quality small molecule drug candidates and to progress these to 
clinical trial. All the scientific disciplines are in place to make this 
possible, including assay development and screening, medicinal chemistry, 
biology, structural biology, metabolism and clinical specialists.
Two postdoctoral positions in Structural Biology (ID 642) and a Higher 
Scientific Officer position in protein production, assay development and 
biophysics (ID 645) are available in Dr Rob van Montfort’s Hit Discovery and 
Structural Design (HDSD) Team within the CTU.

The postdoctoral researchers in structural biology will be involved in X-ray 
crystallography, fragment-based screening and structure-based drug design and 
will be responsible for protein expression, purification, crystallisation, 
structure determination and structural analysis of protein-ligand complexes 
from one of the CTU’s drug discovery programmes. The successful candidates will 
also be part of the Division of Structural Biology, in which the 
crystallographers in Dr van Montfort’s team are embedded, and will have access 
to state of the art crystallisation facilities, an in-house X-ray source and 
excellent access to synchrotrons. The successful candidate will interact 
closely with the biology, computational chemistry and medicinal chemistry teams 
at the CTU, and will therefore be expected to work across the two sites in 
Chelsea, London and Sutton, Surrey. Applicants must have a PhD in a biological 
or physical science, and experience in macromolecular crystallography (to 
include protein biochemistry, protein crystallisation, & protein 
crystallography). Experience in molecular biology, protein expression in insect 
cells, structure-based drug design, and/or biophysics will be an advantage. The 
starting salary for the positions will be in the range £31,023 to £39,473 p.a. 
inclusive (based on previous post-doctoral experience). One position is funded 
for one year and one is funded for two years. Applicants will automatically be 
considered for both positions. Informal enquiries can be made via email to 
rob.vanmontf...@icr.ac.uk or 
yann-vai.lebi...@icr.ac.uk.
The higher scientific Officer protein production, assay development and 
biophysics will be involved in establishing the expression, purification and 
characterisation of one of our early stage drug targets, using contemporary 
expression systems and purification methods available within the HDSD team. The 
postholder will be based in Sutton. In addition, the post-holder is expected to 
characterise ligand and inhibitor binding to the recombinant proteins using 
biochemical assays and biophysical methods such as Thermal-shift assays, 
surface plasmon resonance (SPR), isothermal titration calorimetry (ITC) and 
ligand-based NMR methods. The successful candidate will be an integral member 
of a multidisciplinary project team and will interact closely with the 
biologists, computational chemists, medicinal chemists and structural 
biologists. Applicants must have a BSc in a biochemistry or related biological 
subject and in depth technical laboratory experience in protein expression and 
purification methodologies. Expertise in insect cell expression, assay 
development and/or knowledge of protein NMR methods would be advantageous. The 
starting salary for the position will be in the range of £33,285 to £37,359 
p.a. inclusive (based on previous experience) and the post is offered on a 
fixed term contract of 1 year. Informal enquiries to 
rosemary.bu...@icr.ac.uk or 
rob.vanmontf...@icr.ac.uk

Please DO NOT send your application to Dr van Montfort, Dr Burke or Dr Le 
Bihan. Applications will only be considered if made via the e-recruitment 
system on our website www.icr.ac.uk.

Dr. Rob van Montfort
Team Leader Hit Discovery and Structural Design
Divisions of Cancer Therapeutics and Structural Biology
The Institute of Cancer Research
15 Cotswold Road
Sutton SM2 5NG
UK

Tel:
+44-(0)20-8722-4364 

[ccp4bb] Turning off the bulk solvent modelling in Refmac5 to generate Polder maps?

[Samuel Davis (PG Research)]

Hi,

I'm wondering if anyone knows if it is possible to turn off the bulk solvent 
modelling in Refmac5, for the purpose of generating Polder maps? I know that an 
option for Polder maps is directly implemented in Phenix, but we ideally want 
to use Refmac5, as we have used it for the rest of our refinement and want to 
keep it consistent if possible.

Thanks,

Samuel.

Samuel Davis
MRC 3.5 Year Programme PhD Student
Life Sciences, Biological Chemistry and Drug Discovery, University of Dundee
+44 (0)1382 388325 | swda...@dundee.ac.uk

Scottish University of the Year
The Times / Sunday Times Good University Guide 2016 and 2017

Follow my blog: https://musingsofanearlycareerscientist.wordpress.com

The University of Dundee is a registered Scottish Charity, No: SC015096



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[ccp4bb] PhD studentship at Diamond Light Source and University of Essex: Time-resolved crystallography

[Hough, Mike]

Dear CCP4bbers,

I’d be grateful if you could bring this studentship opportunity to the 
attention of any suitable candidates.


Fully-funded 4 year PhD Studentship: Diamond Light Source and University of 
Essex

Time-resolved synchrotron and XFEL crystallography of metalloenzymes using 
anaerobic photocages


Project outline
X-ray crystallography has been the leading method to understand the structure 
and function of proteins and enzymes for decades. Despite this, it has a key 
limitation in that structures are not time-resolved and so do not represent the 
dynamic and changing nature of a protein’s structure as it carries out its 
function or enzymatic reaction. Time-resolved crystallography is one approach 
for capturing structures of reaction intermediates, though for probing fast 
changes approaches are typically limited to light activated processes.

Metalloproteins are vital to a wide range of biological functions and are 
particularly susceptible to site-specific radiation damage, a problem that is 
considerably worse when working at room temperature. Serial sample delivery and 
the use of photocages to trap and trigger reactions offer a means of resolving 
both of the above challenges, making fast time-resolved experiments applicable 
to a wide range of targets.

In this joint studentship between the University of Essex and Diamond Light 
Source you will perform cutting-edge research in the areas of metalloprotein 
structure determination, serial synchrotron crystallography (SSX), and X-ray 
free electron laser (XFEL) data collection to develop approaches for 
time-resolved SSX at Diamond. To this end you will exploit state-of-the-art 
fixed target instrumentation at Diamond and characterise photocages and their 
activation in crystals. Experiments and developments will be carried out using 
metalloproteins prepared by you at the University of Essex. There will also be
the opportunity to carry out experimental work at the SACLA XFEL in Japan.

You will spend approximately half of the studentship based at the University of 
Essex and half based at Diamond.

We are looking for an exceptional and highly motivated candidate with a good 
Undergraduate or Masters degree in a relevant subject including Life Sciences, 
Physics or Chemistry. A willingness to travel to carry out experimental work at 
international facilities is essential. Start date October 2019.

This interdisciplinary project offers exceptional training opportunities in the 
rapidly developing field of serial and time-resolved structural biology. Full 
training in all required methodology will be provided. The University of Essex 
Proficio scheme offers an extensive range of training courses in transferable 
skills.

Applications should be submitted electronically by the 8th April 2019 see here 
for details 
https://www.essex.ac.uk/pgapply/enter.aspx
 and should state the project title and supervisors. Potential applicants are 
strongly encouraged to informally contact the supervisors in advance: Dr Mike 
Hough (maho...@essex.ac.uk; 
https://www.essex.ac.uk/people/hough20300/mike-hough)
 or Dr Robin Owen (robin.o...@diamond.ac.uk; 
https://www.diamond.ac.uk/Instruments/Mx/I24/Staff/Owen.html)

For general information about the School of Biological Sciences at the 
University of Essex please visit our webpages 
http://www.essex.ac.uk/bs/.
 For information regarding macromolecular crystallography beamlines at Diamond 
please visit 
https://www.diamond.ac.uk/Instruments/Mx
Funding Notes

This is a fully-funded 4-year PhD Studentship covering Home/EU fees and with an 
enhanced stipend.
Please note: International students need to have additional funding to cover 
the difference in tuition fees which is currently £12,410 per year, evidence 
will be requested that you have these additional funds.

Further details are here:
https://www.findaphd.com/phds/project/time-resolved-synchrotron-and-xfel-crystallography-of-metalloenzymes-using-anaerobic-photocages/?p106337\

Many thanks!

Mike




Dr Michael Hough
Senior Lecturer in Structural Biology
School of Biological Sciences
University of Essex
Wivenhoe Park, Colchester
CO4 3SQ
United Kingdom
Phone number: +44 1206 87 3317

[ccp4bb] Hot Topics in Contemporary Crystallography 4 - Structural biology

[Igor Sabljić]

 

Dear colleagues,

We are pleased to announce the registration and bursary applications are
now open for the _Hot Topics in Contemporary Crystallography 4 -
Structural biology_, to be held in the mythic city of Dubrovnik
(Croatia) _from Oct. 1st to 6th, 2019_. Over four intensive days, four
genuinely HOT topics which go beyond classical biomolecular
crystallography, yet complement it smoothly, will be tackled in-depth:
free electron lasers, cryo-EM, NMR in macromolecular research and _in
silico_ simulations. All the details on the workshop (registration,
bursaries, accommodation, venue, travel and commercial partnership) are
just a click away - htcc4.org 

We are very much looking forward to host you in Dubrovnik later this
year! 
-- 

-

IGOR SABLJIĆ [1] 

_Programme coordinator_ 

Hot Topics in Contemporary Crystallography - Structural Biology 

Dubrovnik, Croatia, Oct. 1 - 6, 2018 

T +385 1 456 1025 

W http://htcc4.org [2] 

F https://www.facebook.com/HTCC4/ [3] 

IG https://www.instagram.com/crystallographers.hr/?hl=hr [4] 

-
 

Links:
--
[1] http://www.irb.hr/Ljudi/Igor-Sabljic
[2] http://htcc4.org
[3] https://www.facebook.com/HTCC4/
[4] https://www.instagram.com/crystallographers.hr/?hl=hr



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[ccp4bb] PhD position in Auckland

[Alok Mitra]

Dear Colleagues:
Please ignore if this e.mail is a repeat reception – and apologies then in 
advance.
-
This is to bring to your attention an opening for a PhD student position as 
described below.
A fully Funded Ph.D. position at the School of Biological Sciences, University 
of Auckland and AgResearch, New Zealand

The bacteria derived anti-feeding prophage (Afp) is a unique DNA-free, 
phage-like entity likened to a cell free type 6 secretion system. It is 
pathogenic to a biological pest, the New Zealand pasture (grass grub) by 
transporting and delivering a protein toxin to the grass grub larvae.  In order 
to assess the mechanism of Afp assembly and target cell interaction, we are 
seeking well-qualified and highly motivated candidates for doctoral student 
positions. Using structural, molecular and cell biology, the projects seeks to 
determine and demonstrate the mechanism of Afp cell targeting and toxin 
delivery to the insect grass grub host.
The student will be determining 3-D structures that are 
specifically of cell targeting regions of Afp and that of the Afp toxin. The 
student will have an interest and prior training in cryo electron microscopy 
and/or X ray crystallography. Students with experience in molecular cloning, 
protein expression, purification will be preferred.
The PhD position will be in collaborative dialogue allowing a cross 
fertilization of projects with Dr Mark Hurst AgResearch Lincoln and Dr Alok K. 
Mitra, University of Auckland. Fees and a three-year stipend will be provided 
as part of the New Zealand MBIE endeavour fund contract – “Insect active nano 
machines”.
For further information, please send a current CV containing 3 referee names 
and contact to Dr. Alok K. Mitra, School of Biological Sciences, University of 
Auckland, Auckland, New Zealand. Tel: +64 09 923 8162, E-mail: 
a.mi...@auckland.ac.nz, and  Dr Mark Hurst 
Forage Science AgReserach Lincoln, New Zealand  Tel +64 03 3259919, E-mail:  
mark.hu...@agresearch.co.nz.

Hurst MRH, Beattie A, Jones SA, Laugraud A, van Koten C, Harper L. (2018) 
Serratia proteamaculansstrain AGR96X encodes an antifeeding prophage (Tailocin) 
with activity against grass grub (Costelytra giveni) and manuka beetle 
(Pyronota species) larvae. Appl Environ Microbiol. 84(10). pii: e02739-17. doi: 
10.1128/AEM.02739-17
Rybakova D Radjainia M, Turner A, Sen A, Mitra AK and Hurst MRH. (2013) Role of 
antifeeding prophage (Afp) protein Afp16 in terminating the length of the Afp 
tailocin and stabilizing its sheath. Mol Micro. 89:702–714.
Rybakova D, Schramm P, Mitra AK, Hurst MR. (2015) Afp14 is involved in 
regulating the length of Anti-feeding prophage (Afp). Mol Microbiol. 96: 815-26.
Heymann JB, Bartho JD, Rybakova D, Venugopal HP, Winkler DC, Sen A, Hurst MR, 
Mitra AK (2013) 3-dimensional structure of the toxin-delivery particle 
antifeeding prophage of Serratia entomophila. J Biol Chem. 288: 25276-84
Hurst MRH, Beard SS, Jackson TA, Jones SM. (2007) Isolation and 
characterisation of the Serratia entomophila antifeeding prophage. FEMS 
Microbiol Letts 270:42.

Thank you for your attention
Kind regards
Dr. Alok K. Mitra





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[ccp4bb] [offtopic for ccp4bb] Real space vs reciprocal refinement

[Maheshwaran.V]

Dear all,


In the current version of phenix.refine contains the separate option for
refinement: xyz (reciprocal space) and xyz (real space ).  What does it
mean and how it differs from the previous versions which had xyz and real
space instead.

So I just wanted to know what does it actually do?

Can we run both of them simultaneously?

Is it advisable to do both refinement for DNA ?



-
Mahesh
India.

-- 
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*V . MAHESHWARAN*
SERB-National Post Doctoral Fellow (NPDF)
IMTECH
Chandigarh
India
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