[ccp4bb] PhD studentship in Biological Image Analysis

[Alun Ashton]

(Full details at http://www.nottingham.ac.uk/jobs/currentvacancies/ref/SCI1278)

Applications are invited for a fully-funded PhD studentship to be held jointly 
at the School of Computer Science, University of Nottingham and The Diamond 
Light Source, the UK's national synchrotron facility at Harwell, Oxfordshire. 
Diamond generates brilliant beams of light from infra-red to X-rays which are 
used to acquire images at extremely high resolutions: imaging of sub-cellular 
components of biological objects is a key application of the Diamond facility. 
Analysis of such images requires cell components to be identified and accurate, 
quantitative descriptions of their properties (shape, size, position, etc) 
recovered from the image. The very high spatial and grey-level resolution of 
synchrotron images means that very fine details (of e.g. mitochondria) are 
visible - organelles do not appear as simple, evenly coloured regions but as 
highly variable, textured areas. This PhD project seeks to develop automatic 
image analysis methods and software tools that can extract quantitative 
measurements of sub-cellular objects from Diamond Light images. The successful 
student will work closely with research staff and potential users at both 
Nottingham and Diamond.
 
Students should have a good first degree (preferably at the level of a 
first-class degree in the UK context) in Computer Science or a related 
discipline. Previous experience of image analysis, computer vision or 
biological science are an advantage, but not essential. 
 
Informal enquiries may be addressed to:
 Dr Andrew French: andrew.p.french @ nottingham.ac.uk
 Dr Mark Basham: Mark.Basham @ diamond.ac.uk
 Dr Tony Pridmore: tony.pridmore @ nottingham.ac.uk
 
Details on how to apply are on the website. 

Alun Ashton
___
Alun Ashton, alun.ash...@diamond.ac.uk Tel: +44 1235 778404
Group Leader - Data Analysis Software,www.diamond.ac.uk 
Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K.





-- 

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] CCP4 Newsletter 49

[Karen McIntyre]

Dear BB members

The latest issue of the CCP4 newsletter is now available at 
http://www.ccp4.ac.uk/newsletters.php .

Regards

Karen McIntyre
Scientific Computing Department - CCP4
R92 1.22 RCaH

Science & Technology Facilities Council
Rutherford Appleton Laboratory
Harwell Science & Innovation Campus
Didcot
Oxfordshire
OX11 0FA

Tel +44 (0) 1235 44 5790
Fax  +44 (0) 1235 56 7720

**Please note that I only work mornings until 12.45pm**


-- 
Scanned by iCritical.

Re: [ccp4bb] TLS refinement refmac

[Eleanor Dodson]

Well - most refinement procedures output the Fobs and the Fcalc on the same
(more-or-less) absolute scale..

After data processing the observations are on a more or less arbitrary
scale, so that seems sensible.

It gets more problematic when you start correcting for anisotropy..
Eleanor




On 17 July 2013 15:59, Phoebe A. Rice  wrote:

>  EEK, it seems to me that anything called simply "FP" should be
> unadulterated FP.  If the software modifies a column in some way, it should
> give it a new label, shouldn't it?
>
>  ++
>
> Phoebe A. Rice
> Dept. of Biochemistry & Molecular Biology
> The University of Chicago
>
> 773 834 1723; pr...@uchicago.edu
> http://bmb.bsd.uchicago.edu/Faculty_and_Research/
>
> http://www.rsc.org/shop/books/2008/9780854042722.asp
>   --
> *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor
> Dodson [eleanor.dod...@york.ac.uk]
> *Sent:* Wednesday, July 17, 2013 6:05 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] TLS refinement refmac
>
>Oh dear - you should always start refinement against the original
> processed data - but others have told you that already..
>
>  The TLS files will not be appropriate for the rescaled FPs - it is
> surprising that the Rfactor actually goes down though!
>  Or are you doing several cycles of refinement in thesecond pass too - in
> that case one would hope the Rfactor would continue to fall.
>  Eleanor
>
>
>
>
> On 17 July 2013 11:00, Guenter Fritz wrote:
>
>> Am 17.07.2013 11:59, schrieb Guenter Fritz:
>>
>>> Hi Stefan and Gottfried,
>>> thanks a lot for the answers. This is the point. Wouldn't it make more
>>> sense to add an extra column that contains the changed Fs?
>>> Best, Guenter
>>>
>>>  Hi,

 it is strongly advised to use the original mtz e.g. scala.mtz as the
 refmac input mtz in all refmac runs,
 as this contains the original Fs - Refmac applies some aniso
 corrections  to the Fs and puts them into the output.mtz.

 so the output Fs are not the same as in the input F - therefore one
 should use the scala.mtz

 cheers
 Stefan


 -Ursprüngliche Nachricht-
 Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
 Guenter Fritz
 Gesendet: Mittwoch, 17. Juli 2013 10:39
 An: CCP4BB@JISCMAIL.AC.UK
 Betreff: [ccp4bb] TLS refinement refmac


 Dear all,

 one gets different R values, if you re-read in the mtz written out by
 refmac after TLS refinement. I think this issue had been a while ago in
 ccp4bb, but I can't find the right track.

 Here are the details.

 1st run:
 If we do TLS + restr. refinement in refmac we get:
 InitialFinal
 R factor0.3010   0.2170
 R free0.3175   0.2695

 2nd run:
 Now, if we use the same input pdb and the same input tls paramter file,
 but use the mtz written out by the first run, we get:
 InitialFinal
 R factor0.2274   0.1903
 R free0.2482   0.2540


 Apparently in the mtz file written out by the 1st refmac must contain
 some information that is re-read in the 2nd run. But one just defines
 FP, SIGFP and Rfree flags. Do FPs change in the output mtz after TLS
 refinement??

 Any help to clarify this is appreciated.

 Thanks, Guenter

>>>
>>>
>

[ccp4bb] Off-topic post: Inverted DNA repeats vs direct repeats

[Raji Edayathumangalam]

Hi Everyone,

One of the proteins I work with is a transcription factor that binds to two
direct repeats in its cognate binding site. That my protein binds direct
repeats is unlike most other members of its family that bind to inverted
repeats. One of the reviewers of a paper that my colleagues and I submitted
would like to know what the significance of having a direct repeat is vs.
an inverted repeat is.

So I dug around and learned the following about inverted repeats:
(1) Inverted repeats can form intramolecular hairpin or cruciform
structures.
(2) Inverted repeats play diverse roles in biological processes (DNA
replication, transcriptional regulation, translational control etc).
(3) Inverted repeats can cause genome instability and genomic
rearrangements.
(4) Inverted repeats are associated with several human diseases.

Is there anything known about whether one type of repeat or the other
predominates in nature?

Is anyone able to add anything more than the above about the particular
significance of why nature may have chosen a direct repeat in the case of
my protein instead of an inverted repeat?

Also, any pointers towards relevant literature would be great. My searches
thus far haven't yielded much more than what I've shared above.

Many thanks!
Raji

-- 
Raji Edayathumangalam
Instructor in Neurology, Harvard Medical School
Research Associate, Brigham and Women's Hospital
Visiting Research Scholar, Brandeis University

[ccp4bb] post-doctoral in membrane protein structural biology

[Pascal Egea]

We are seeking a post-doctoral researcher to join my research group at
UCLA. The lab focuses on the structural studies of challenging targets:
membrane protein complexes and channels from eukaryotes (yeast and several
parasites) and seeks to characterize their architecture and molecular
mechanisms of action combining X-ray crystallography, SAXS and cryo-EM when
necessary and possible.

 We will exclusively consider applicants with proven experience in
protein crystallography, cloning, protein expression and purification. Previous
experience with membrane proteins is highly desirable but not required.
Candidates should hold or expected to soon hold a PhD degree in a relevant
area (Biophysics, Structural Biology) and have excellent social and
communication skills in english (very important). Interested candidates
should send a CV and personal statement together with the name and
addresses of three references.

   I will be attending the ACA-2013 meeting in Hawaii this coming week and
will present a poster presented from 5:30-07:30pm on Sunday, July 21.
Motivated individuals are invited to directly contact with me.


Pascal F. Egea, PhD
-
Assistant Professor
UCLA, David Geffen School of Medicine
Department of Biological Chemistry
Boyer Hall room 356
611 Charles E Young Drive East
Los Angeles CA 90095
office (310)-983-3515
lab  (310)-983-3516
email pe...@mednet.ucla.edu

[ccp4bb] PhD student position in Structural Biology at University of Bayreuth

[Michael Weyand]

**We are currently looking for a highly motivated Ph.D. student for our
laboratory at the Dept. of Biochemistry at University Bayreuth, Germany.
Our work involves biochemical and structural studies on cellular
signalling systems with relevance to aging mechanisms or disease. The
PhD project will comprise biochemical and structural studies on either
cyclic nucleotide signalling or deacetylases of the Sirtuin family (for
related publications, see, e.g., PNAS 105, 15720-5; J Biol Chem. 2011
Sep 2;286(35):30423-32; PLoS One. 2012;7(11):e49761;
http://www.pnas.org/content/early/2013/07/09/1303628110.abstract
).

Our laboratory is located in a brand new building at the University of
Bayreuth and equipped with state-of-the-art facilities for protein
biochemistry, x-ray crystallography, and mass spectrometry. We offer
excellent research opportunities and a stimulating environment for
research in structural biology.

The ideal candidate is a highly motivated student with strong interest
in structural biology and prior experience in protein biochemistry.
Additional experience in molecular biology and/or protein
crystallization would be an asset.

Applications (including CV, research experience, and two names and
contact information for references) should be sent as PDF or by mail to

/Prof. Dr. Clemens Steegborn /

/University of Bayreuth /

/Dept. Biochemistry, NW III
Universitaetsstr. 30
95447 Bayreuth, Germany/

/ /

/phone: ++49 0921 / 55 - 7831/

/email:  //sekretariat.bioche...@uni-bayreuth.de/
//

/web://www.biochemie.uni-bayreuth.de/

Re: [ccp4bb] Dose anyone see this ligand before?

[Wei Feng]

Dear Dale Tronrud,
Thanks for your advise. Initially, i focused on the shape of the density. As 
you suggest, i checked all possible biological molecules and common additives 
used in purification and crystallization. I found that the structure of 
bis-tris-propane is similar to the target density. And the environment of 
crystallization contain this molecular. So, i will try it. Thanks again!
Wei








At 2013-07-18 02:20:10,"Dale Tronrud"  wrote:
>
>Do you have any reason to expect either of these molecules would be in
>your crystal?   The model you build has to fit the density, be consistent with
>the surrounding environment (which you haven't shared with us) and you
>have to have some story for how that molecule got in your crystal.  Personally
>I would steer away from industrial compounds and focus more on biological
>molecules and common additives used in purification and crystallization.
>
>The environment is critical to identifying this molecule.  What hydrogen 
> bonds
>does this molecule make?  What charges are near by?  Certainly the presence
>or absence of hydrogen bonds will distinguish between these two compounds
>before you go to the trouble to build a model of either.
>
>Dale Tronrud
>
>On 7/17/2013 6:35 AM, Wei Feng wrote:
>> Dear all,
>> Thank you for your advices.
>> I had tried to use MPD and pyrophosphate etc to fix the density map but all 
>> of them were too small.
>> We guess that the molecular formula should be C8H18O2. So we search this 
>> formula in google and find two candidate molecules
>> 1: http://flyingexport.en.ecplaza.net/dhad-99-5--137042-689140.html
>> 2: http://en.m.wikipedia.org/wiki/Di-tert-butyl_peroxide
>> Could you tell me how to get the coordinate of these molecules?
>> Thank you for your time!
>> Wei
>>
>>
>>
>>
>

[ccp4bb] Of topic, trying to identify a reference for multiple crystal data collection

[Edward Snell]

Dear All,

On a beamline visit I came across a photocopy of a table comprising point 
groups, number of random images and the percentage completeness that resulted. 
The Table is labeled 17.1 and the table legend starts with the text "Data from 
randomly oriented images. The figures shown are the percentage completeness to 
3A resolution. These were calculated by predicting reflections from 90 images 
with randomly generated mis-setting angles, arbitrary cell, wavelength of 0.9A 
and oscillation range of 0.4 degree. Only reflections more than 50% recorded 
were accepted  The figures are essentially independent of resolution. 

I would very much like to reference this but I don't have any idea where it 
came from other than the number 17.1 suggesting it is a rather large book - 
there were no details on the copy. If you recognize this table and could 
provide the reference I'd be very grateful. If I should have read your book 
where it appeared I apologize! I doubt the board would be interested in this so 
please send me a reply offline.

Thanks.

Eddie

Edward Snell Ph.D.
Assistant Prof. Department of Structural Biology, SUNY Buffalo,
Senior Scientist, Hauptman-Woodward Medical Research Institute
700 Ellicott Street, Buffalo, NY 14203-1102
Phone: (716) 898 8631 Fax: (716) 898 8660
Skype:  eddie.snell Email: esn...@hwi.buffalo.edu
Telepathy: 42.2 GHz

Heisenberg was probably here!

[ccp4bb] 71st Annual Pittsburgh Diffraction Conference

[Edward Snell]

Dear All,

The 71st Annual Pittsburgh Diffraction Conference will be being held at the 
Hauptman-Woodward Medical Research Institute from the evening of the 18th of 
September to the afternoon of the 20th. Preliminary details are at 
http://www.pittdifsoc.org/PDC_2013/pittsburgh_diffraction_flyer.pdf and a full 
program will be released shortly. Program topics include crystallization 
approaches for recalcitrant proteins and protein complexes, structural biology 
from an industrial perspective, macromolecular design and DNA nanotechnology, 
technology developments for diffraction methods and a small molecule 
diffraction session. We encourage students to attend and have dedicated 
presentation opportunities. Meeting registration and discount hotel 
registration deadlines are the 16th and 21st of August. Please save the date 
and come enjoy Buffalo, only a short drive from Niagara Falls.

For more information contact the organizers at pdiffract...@hwi.buffalo.edu

Sincerely,

Eddie Snell

Edward Snell Ph.D.
Assistant Prof. Department of Structural Biology, SUNY Buffalo,
Senior Scientist, Hauptman-Woodward Medical Research Institute
700 Ellicott Street, Buffalo, NY 14203-1102
Phone: (716) 898 8631 Fax: (716) 898 8660
Skype:  eddie.snell Email: esn...@hwi.buffalo.edu
Telepathy: 42.2 GHz

Heisenberg was probably here!