[ccp4bb] Postdoctoral Position available - Long Island, New York

2017-10-20 Thread Steven Glynn 
A postdoctoral position is available in the laboratory of Dr. Steven Glynn
at Stony Brook University (*https://you.stonybrook.edu/glynnlab
*). We are looking for a highly
motivated individual to participate in a collaborative research project to
determine the structure and mechanism of proteases that regulate protein
quality control in mitochondria.



https://www.nature.com/articles/ncomms13301

https://www.ncbi.nlm.nih.gov/pubmed/28214511

https://www.biorxiv.org/content/early/2017/09/15/189316



The candidate should hold a Ph. D in Biochemistry, Structural Biology or
related field in hand by January 1, 2018. Qualified applicants will have
demonstrated experience in molecular biology, and protein expression and
purification. Experience in protein structure determination, enzyme
activity assays, and yeast protein expression is preferred.



The Glynn Lab is located at Stony Brook University, 60 miles from New York
City on Long Island's scenic North Shore. We have access to state of the
art facilities in enzymology and structural biology, including the nearby
National Synchrotron Light Source II.  The 1,100-acre campus is home to
24,000 undergraduate, graduate, and doctoral students and more than 13,500
faculty and staff, including those employed at Stony Brook Medicine.



Interested applicants should apply at:

https://stonybrooku.taleo.net/careersection/jobdetail.ftl?job=1700692&tz=GMT-04:00&lang=en



or by visiting http://www.stonybrook.edu/hr/prospective-employees.shtml and
applying to position *1700692*



The posting is available until October 31st. Inquiries may be sent to
steven.gl...@stonybrook.edu

-- 
Steven E. Glynn, PhD
Assistant Professor
Department of Biochemistry and Cell Biology
Stony Brook University
148 Centers for Molecular Medicine
Stony Brook, NY 11794-5115
Tel: 631-632-1055

Re: [ccp4bb] solution for the ref format problem

2017-10-20 Thread Phil 
It’s probably better to combine the MTZ files with Pointless rather than 
sortmtz as that will also check the point group
Phil

Sent from my iPhone

> On 20 Oct 2017, at 18:57, Gottfried Palm  wrote:
> 
> Dear all,
>   technically, the ccp4bb (especially Conn Mallett and Jim Pflugrath) helped 
> to resolve the problem: The procedure to get ccp4-readable data from the .ref 
> files uses dtreflnmerge (provided as part of CrystalClear / d*trek from 
> Rigaku) from the command line, for example:
> 
> dtreflnmerge.exe dtprofit.ref dtprofit_ascii.ref -ascii
> 
> These .ref files could be converted by dtrek2scala to an mtz file in ccp4.
> These mtz files (one for every scan) were merged with sortmtz.
> The sorted multibatch mtz file was scaled with aimless.
> 
> The structure was not solvable, though, which is a bit puzzling to me, 
> because the diffraction pattern is clean to better than 1 A resolution, the 
> unit cell only ca. 1000 cubic Angstrom (small molecule) and the crystals 
> contain Pd with an organic ligand. I am thus still wondering, if something 
> gets messed up in this procedure. I have also tried processing with xds, 
> mosflm and xia2 dials, they failed at indexing. I don't have the resources to 
> figure this out soon, but anybody, who is curious to try the processing is 
> welcome. Contact me directly in December, success will be duly acknowledged.
> 
> Greetings
>   Gottfried
> 
> original post:
> 
> Problem with ref format (Rigaku)
> 
> Dear all,
> 
>   this is a question about scaling data integrated in CrystalClear (Rigaku 
> data processing gui based on d*trek) in ccp4.
> Since scaling dtprofit.ref files from different scans is sometimes poor or 
> even failing within CrystalClear (i.e. with dtscaleaverage after merging 
> them), I used to try scaling them with scala. I am facing this problem mainly 
> with high resolution / small molecule data collection, where I need up to 20 
> scans, each 90-180 degrees, for complete low and high resolution.
> 
> The procedure, that worked, was using
> 
> dtrek2scala for each scan (with scan1.ref and output_scan1.head, then a 
> second run of dtrek2scala for scan2.ref and output_scan2.head, etc.) to 
> create scan1.mtz, scan2.mtz, etc.
> sortmtz with scan1.mtz, scan2.mtz, ... to create a multibatch mtz file
> scala with the multibatch.mtz file to create the final scaled mtz file
> 
> Some time ago Rigaku changed the format of the .ref files, so dtrek2scala is 
> not working any more.
> Is there a possibility to change the new .ref format to the old one? Or can I 
> read the new .ref files in scala or better aimless directly?
> 
> The alternative to process the images in xds hits a similar problem: The 
> format of the images has also changed and the new .img files (from the 
> Saturn92 detector) are not read anymore (whereas they used to be processable 
> in xds before).
> 
> Greetings
>   Gottfried
> 
> 
> Dr. Gottfried Palm
> Ernst-Moritz-Arndt-UniversitÀt
> Inst. für Biochemie (MNF)
> Abt. Biochemie I
> Felix-Hausdorff-Straße 4
> 17489 Greifswald

Re: [ccp4bb] Job opening: Postdoctoral Fellow in Structural Biology and Drug Discovery

2017-10-20 Thread Schonbrunn, Ernst 
Dear Madam/Sir,

Please post the following open postdoctoral position on your job-board.

Thank you,

Ernst Schonbrunn

---
Postdoctoral Fellow in Structural Biology and Drug Discovery

Location: Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612
Department: Drug Discovery Department
Job Details:

Moffitt Cancer Center is internationally recognized for our focus on 
personalized cancer care and translational research. The mission of Moffitt is 
clear, focused, and fully stated in nine words, "To contribute to the 
prevention and cure of cancer." With a tradition of excellence that began with 
the first patient admission in 1986, dedicated Moffitt physicians, scientists, 
and staff members have remained committed to excellence in an atmosphere 
characterized by kindness, caring, and hope.

The Schönbrunn lab studies the structure-function relationship of medicinally 
relevant proteins along with the discovery and development of novel small 
molecule inhibitors as therapeutics.  We are involved in multiple projects 
working in team with medicinal chemists, biologists and clinicians on the 
targeting of proteins involved in cell signaling and epigenetic events. For an 
overview of our research approach and current projects please visit our web 
site at 
labpages2.moffitt.org/schonbrunn/.

 Position Highlights:


· We seek highly motivated postdoctoral researchers to work on 
inter-disciplinary projects towards the characterization and inhibitor 
development of diverse kinases and bromodomain-containing proteins.
*  The position provides exciting opportunities for biochemical, structural 
and cell-based studies of various drug-target interactions and rational drug 
design.

 The Ideal Candidate:


· The ideal candidate has a Ph.D. degree in Biochemistry, Biology, 
Chemistry, Physics or related field and expertise in protein crystallography 
and biochemistry as demonstrated by publications in internationally recognized 
scientific journals.
*  Additional experience in cell biology is preferred.

 Responsibilities:


· Candidates must be enthusiastic and dedicated to science with 
excellent organizational skills and effective at working independently, while 
also collaborating and assisting the team in its collective research goals.
*  Attention to detail and ability to work on multiple projects is required.
*  Excellent verbal and written communication skills are required.

 Credentials and Qualifications:

*  Ph.D. degree in Biochemistry, Biology, Chemistry, Physics or related 
field.

A competitive salary and benefits package will be offered to the successful 
candidate. Interested applicants should send a single PDF file that includes a 
current CV with recent publications, a personal statement of scientific 
interests and goals (2-page maximum) and contact information for three 
references to Dr. Ernst Schönbrunn at 
ernst.schonbr...@moffitt.org

Equal Employment Opportunity
Moffitt Cancer Center is an Equal Opportunity/Affirmative Action Employer. All 
qualified applicants will receive consideration for employment without regard 
to race, color, religion, sex, sexual orientation, gender identity, national 
origin, age, or protected veteran or disabled status. We seek candidates whose 
skills, and personal and professional experience, have prepared them to 
contribute to our commitment to diversity and excellence.




[MOFFITT_2c_RGB for signature]

Ernst Schönbrunn, PhD
Associate Professor
Moffitt Cancer Center

12902 Magnolia Drive, Tampa, FL 33612 | tel:  813-745-4703 | email: 
ernst.schonbr...@moffitt.org




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Thank you.

Re: [ccp4bb] PDB-REDO

2017-10-20 Thread Robbie Joosten 
Hi Florian,



Have a look at the outlier rejection Phenix uses for reflections. You may have 
a few dodgy reflections that mess up the maps. That can give weird ‘layered’ 
maps.



Cheers,

Robbie



Sent from my Windows 10 phone



From: Florian Schubot
Sent: vrijdag 20 oktober 2017 19:19
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] PDB-REDO



Hi,
for the past few weeks we have been trying to use the PDB-redo server to 
improve our refinement of two different structures.  We usually use PHENIX.  
Consistently PDB-REDO gives much better stats (Rfree <025 vs 0.28 with PHENIX) 
BUT the resulting electron density maps are clearly worse. It looks warped.  I 
was curious if somebody has had a similar experience or if there is something 
particular I need to do when viewing the maps in COOT.
Thank you,
Florian

[ccp4bb] PDB-REDO

2017-10-20 Thread Florian Schubot 
Hi,
for the past few weeks we have been trying to use the PDB-redo server to 
improve our refinement of two different structures.  We usually use PHENIX.  
Consistently PDB-REDO gives much better stats (Rfree <025 vs 0.28 with PHENIX) 
BUT the resulting electron density maps are clearly worse. It looks warped.  I 
was curious if somebody has had a similar experience or if there is something 
particular I need to do when viewing the maps in COOT.
Thank you,
Florian

[ccp4bb] solution for the ref format problem

2017-10-20 Thread Gottfried Palm 

Dear all,
  technically, the ccp4bb (especially Conn Mallett and Jim Pflugrath) 
helped to resolve the problem: The procedure to get ccp4-readable data 
from the .ref files uses dtreflnmerge (provided as part of CrystalClear 
/ d*trek from Rigaku) from the command line, for example:


dtreflnmerge.exe dtprofit.ref dtprofit_ascii.ref -ascii

These .ref files could be converted by dtrek2scala to an mtz file in ccp4.
These mtz files (one for every scan) were merged with sortmtz.
The sorted multibatch mtz file was scaled with aimless.

The structure was not solvable, though, which is a bit puzzling to me, 
because the diffraction pattern is clean to better than 1 A resolution, 
the unit cell only ca. 1000 cubic Angstrom (small molecule) and the 
crystals contain Pd with an organic ligand. I am thus still wondering, 
if something gets messed up in this procedure. I have also tried 
processing with xds, mosflm and xia2 dials, they failed at indexing. I 
don't have the resources to figure this out soon, but anybody, who is 
curious to try the processing is welcome. Contact me directly in 
December, success will be duly acknowledged.


Greetings
  Gottfried

original post:

Problem with ref format (Rigaku)

Dear all,

  this is a question about scaling data integrated in CrystalClear 
(Rigaku data processing gui based on d*trek) in ccp4.
Since scaling dtprofit.ref files from different scans is sometimes poor 
or even failing within CrystalClear (i.e. with dtscaleaverage after 
merging them), I used to try scaling them with scala. I am facing this 
problem mainly with high resolution / small molecule data collection, 
where I need up to 20 scans, each 90-180 degrees, for complete low and 
high resolution.


The procedure, that worked, was using

dtrek2scala for each scan (with scan1.ref and output_scan1.head, then a 
second run of dtrek2scala for scan2.ref and output_scan2.head, etc.) to 
create scan1.mtz, scan2.mtz, etc.

sortmtz with scan1.mtz, scan2.mtz, ... to create a multibatch mtz file
scala with the multibatch.mtz file to create the final scaled mtz file

Some time ago Rigaku changed the format of the .ref files, so 
dtrek2scala is not working any more.
Is there a possibility to change the new .ref format to the old one? Or 
can I read the new .ref files in scala or better aimless directly?


The alternative to process the images in xds hits a similar problem: The 
format of the images has also changed and the new .img files (from the 
Saturn92 detector) are not read anymore (whereas they used to be 
processable in xds before).


Greetings
  Gottfried


Dr. Gottfried Palm
Ernst-Moritz-Arndt-UniversitÀt
Inst. für Biochemie (MNF)
Abt. Biochemie I
Felix-Hausdorff-Straße 4
17489 Greifswald

[ccp4bb] combining partial reflection datasets in pointless

2017-10-20 Thread John Beale 
Hello all,

I have been trying to combine many small wedges in pointless. These data have 
been processed in dials and exported to mtz using either the flags 
keep_partials or keep_partials and include_partials (the same wedge of data 
exported using these two methods are attached).

Pointless will happily read the keep_include_partial mtz (approx. 7000 
reflections) but will not read the keep_partial mtz (approx. 14000 
reflections). A segmentation fault occurs.

If anyone one has any thoughts as to why this is the case, I would be very 
grateful for your ideas.

John

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[ccp4bb] HERCULES 2018-Neutron & Synchrotron European School for Physics, Chemistry & Biology - [updated deadline: 25 October 2017]

2017-10-20 Thread David Flot 





 Forwarded Message 
Subject: 	HERCULES 2018-Neutron & Synchrotron European School for 
Physics, Chemistry & Biology - [updated deadline: 25 October 2017]

Date:   Thu, 12 Oct 2017 12:25:49 +0200
From:   Vincent Favre-Nicolin 
Reply-To:   HERCULES SCHOOL 
To: 	hercules-...@listes.grenoble.cnrs.fr 





*HERCULES 2018**- European School*
/28 Years of Neutron & Synchrotron Radiation Science/

*2018 **session**:**/   25 February-30 March, 2018/*
/*UPDATED DEADLINE FOR APPLICATION: 25 October 2017*/

    HERCULES is a European course for PhD students and young 
researchers using *Neutrons* and *Synchrotron Radiation* for 
applications in *Biology*, *Chemistry*, *Physics*, *Hard & Soft 
Condensed Matter*.


    The 1-month school includes *lectures* (60%), *hands-on practicals* 
and *tutorials* at partner institutes (*Elettra* and *FERMI* in Trieste, 
Italy, *ESRF*, *ILL* in Grenoble, *Soleil* and *LLB* in Paris-Saclay, 
*PSI* in Villigen, Switzerland) and Grenoble Laboratories (CEA, CNRS, 
EMBL, IBS). (*)
(*)  also, participation of DESY and the European XFEL to be confirmed 
for 2018 due to scheduled down-time.


    The school  includes a common part and two parallel sessions:
- /*Biomolecular, soft condensed matter structure & dynamics*/
- /*Physics and chemistry of condensed matter*/
*

/    Why join Hercules//?
/*- to *learn new techniques using neutron and synchrotron radiation*
- to expand your *theoretical *and*practical *knowledge, /not only for 
your present research but for your scientific career/

- to *experiment these techniques* on world-class instruments & beamlines
- to build a network of relations with fellow young researchers and 
experienced teachers from all around the World


/*Bursaries/reduced costs*/
- A limited number of bursaries will be available either to reduce 
registration fees or cover travel costs.


***/More information/**:* (see programme overview below)

 * Hercules website: http://hercules-school.eu/
 * Full list of lectures: http://hercules-school.eu/24-session-program.htm
 * Download the full 2017 Booklet (lectures, practicals..)
   




Contact email: hercu...@hercules-school.eu 





   Programme


   Common Lectures://
   


 * Interaction of X-rays and neutrons with matter (absorption, elastic
   and inelastic interactions, ...)
 * Sources (neutron, synchrotron, XFEL)
 * Detectors
 * Optics &instrumentation
 * Diffraction (single crystal, powder..)
 * Scattering (elastic, inelastic..)
 * Spectroscopy
 * Imaging (Absorption, coherent,..)

*Session: Applications to Biomolecular, Soft Condensed matter  Structure 
and Dynamics*


 * Protein structure and dynamics
 * Studies in solutions
 * Partially ordered systems
 * Membranes, fibres and muscles
 * Crystallography of large structures (viruses,...)
 * Structural genomics
 * Biomedical applications (imaging, therapy)
 * Time-resolved and ultra-fast X-ray science
 * Biology with 4th generation sources
 * ...

*Session: Applications to Physics and Chemistry of Condensed Matter*

 * Neutron and X-ray (and UV and IR) spectroscopies
 * X-ray reflectivity and diffraction of nano systems
 * Single crystal and powder diffraction
 * Coherent imaging and tomography
 * Neutron and X-ray magnetic scattering
 * Polarized X-rays and neutrons
 * FEL and ultra fast X-ray science
 * ...



To no longer receive information about HERCULES, use the following link:
https://listes.grenoble.cnrs.fr/sympa/auto_signoff/hercules-has/re...@esrf.fr

--
Vincent Favre-Nicolin

Co-editor, J. Synchrotron Radiationhttp://journals.iucr.org/s/

Director, HERCULES schoolhttp://hercules-school.eu

ESRF-The EuropeanSynchrotronhttp://www.esrf.eu
71, Avenue des Martyrs
Grenoble, France

X-Ray NanoProbe (XNP) group

Tel: +33 4 76 88 28 11

On leave from Univ. Grenoble Alpes