[ccp4bb] UK/Japan "dynamic crystallography" meeting Leicester UK Sept 14 & 15

[Peter Moody]

We are delighted to announce #time_resolved_23
Find out more and register through https://timeresolved23.le.ac.uk/

*Dynamic Crystallography - XFELs and Synchrotrons to study enzyme reactions
 13-15 September, Leicester, UK*



The  meeting is sponsored by the UK’s BBSRC Japan Partnering Award Scheme,
the meeting aims to bring researchers from Japan who are developing and
using techniques to exploit XFELs and synchrotrons for time-resolved
studies of enzyme mechanisms together with researchers from the UK and our
partners with similar interests to present and discuss prospects, progress
and, of course, results. All with a view to establishing and furthering
collaborations.







The current planned outline of the meeting/workshop is:  (see the meeting
website timeresolved23.le.ac.uk for updates)



*Thursday 14 September *

*Preparation* – How to make suitable samples to enable the study of
transient or short-lived enzyme reaction stats

*Validation* – How to monitor reactions in crystals

*Data Collection* – Strategies and protocols for the collection of
diffraction and spectroscopic data



*Friday 15 September *

*Data Processing* – Strategies, and protocols for the optimal recovery of
high-quality data

*Analysis and interpretation* – How to overcome temporal uncertainty with
respect to reaction coordinates and how to interpret mixed populations.

*Results *– Examples of the application of dynamic investigation of protein
mechanisms using structural and spectroscopic techniques.



At the time of writing  we have the following colleagues from Japan who
will participate (with titles of contributions where we have them):

   -
  - * Hiroshi Sugimoto* (SACLA Spring-8/RIKEN) “Dynamics of hydrogen
  atom revealed by ultra-high resolution structure of the heme acquisition
  protein”
  - *Takehiko Tosha* (University of Hyogo) “Characterization of the
  short-lived reaction intermediate of NO reductase with caged substrate”
  - *Yoshitsugu Shiro* (University of Hyogo)
  - *Hitomi Sawai* (University of Nakasaki)
  - *Michihiro Suga* (Okayama University)
  - *Minoru Kubo* (University of Hyogo) “Time resolved spectroscopy for
  monitoring the protein dynamics in microcrystals”
  - *Tetsuo Katayama (Japan Synchrotron Radiation Research
Institute) *"Instrumental
  development and data analysis of X-ray emission spectroscopy
supporting SFX
  at SACLA"
  - * Tetsunari Kimura* (Kobe University) “Development of the
  microfluidic mixer for time-resolved SFX and spectroscopy”

   Speakers from Europe we currently have confirmed:
   - * Allen Orville* (XFEL Hub at Diamond Light Source)
  - * Ivo Tews* (University of Southampton)
  - * Mike Hough* (Diamond Light Source)*Dr Briony Yorke* (University
  of Leeds)  "Developing multiplexing methods for time-resolved
  crystallographic experiments"
  - *Robin Owen* (Diamond Light Source) “Efficient sample delivery for
  time resolved SSX and SFX” (TBC)
  - *Thomas Ursby *(MAX IV Laboratory) "Serial Crystallography at
  MicroMAX - Flexibility offering new possibilities"
  - *Emily Freeman* (University of Oxford) “Time-resolved
  macromolecular crystallography studies of AmpC from *Escherichia
coli* using
  synchrotron and XFEL radiation”.
  - *Jack Stubbs* (University of Southampton and Diamond Light Source)
  "Size matters: Microfluidics for defining protein crystal dimensions and
  rapid micromixing for time-resolved serial crystallography"
  - *Patrick Shaw Stewart *(Douglas Instruments) "Preparing crystal
  samples for serial data collection and microED: using microseeding and
  phase diagrams with microbatch-under-oil"
  - *James Beilsten- Edmands* (Diamond Light Source) “Processing serial
  diffraction data with DIALS & xia2”.
  - *Marcus Gallagher-Jones* (Rosalind Franklin Institute)
  - *Thomas Barends* (MPI-IMF Heidelberg)


Please don't use "reply to" with this email, if you want to get in touch
with me use my university email address  peter.moody at le.ac.uk



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[ccp4bb] 12 month post-doc in Leicester on enzyme intermediates with Peter Moody

[Peter Moody]

I have 12 months BBSRC-funded support available for a PDRA in Leicester.
This might suit someone who has still to finish writing up or being
examined for their PhD, I am happy to discuss some flexibility.  The post
is available from 1 January until the end of December 2022.
The research (in collaboration with the Co-I Prof Emma Raven, now at the
Chemistry Department of the University of Bristol) is to understand heme
peroxidase enzyme mechanism. For this we need to trap intermediates and
determine the structures. There is controversy over the nature of these
intermediates and we have used tools such as neutron crystallography and
X-ray free electron lasers in the past which have resulted in high-impact
publications. Specific remaining aims of this project include the direct
determination of the protonation state of the Compound II intermediate of
cytochrome c peroxidase using neutron crystallography and of the myoglobin
analogue using neutron and XFEL techniques. We are also developing
techniques for using microcrystal electron diffraction to study enzyme
intermediates. We are interested in using a wide variety of biochemical and
biophysical techniques to complement and verify the studies. This includes
UV-Visible and X-ray spectroscopy. The group (
https://le.ac.uk/liscb/research-groups/peter-moody) is based in the
Leicester Institute for Structural and Chemical Biology (
https://le.ac.uk/liscb ), a supportive and collegiate environment with
access to world-class facilities and expertise.
This post is suitable for someone interested in expanding their experience
of, and pushing the boundaries of, methods to understand enzyme mechanisms.
You will be competent working with proteins in the laboratory and want to
learn about and apply physical and chemical techniques to biological
problems

Please contact me using my university email, peter.moody @ le.ac.uk
(without the spaces), do not reply to this email directly.

These papers are some recent examples of our work:

1. H Kwon, J Basran, C Pathak, M Hussain, SL Freeman, AJ Fielding, AJ
Bailey, N Stefanou, HA Sparkes, T Tosha, K Yamashita, K Hirata, H Murakami,
G Ueno, H Ago, K Tono, M Yamamoto, H Sawai, Y Shiro, H Sugimoto, E Raven &
PCE Moody (2021) XFEL Crystal Structures of Peroxidase Compound II XFEL
Crystal Structures of Peroxidase Compound II. Angewandte Chemie Int.
Edition doi: 10.1002/anie.202103010

2. H Kwon, J Basran, CM Casadei, AJ Fielding, TE Schrader, A Ostermann, JM
Devos, P Aller, MP Blakeley, PCE Moody & EL Raven (2016) Direct
visualization of a Fe(IV)–OH intermediate in a heme enzyme Nature
Communications 7, Article number: 13445 (2016)

3. H Kwon, J Basran, J M. Devos, R Suardiaz, MW van der Kamp, AJ
Mulholland, TE Schrader, Andreas Ostermann, Matthew P. Blakeley, Peter C.
E. Moody & Emma L. Raven (2020) Visualizing the protons in a metalloenzyme
electron proton transfer pathway. Proc. Natl. Acad Sci. (USA) 117 (12)
6484-6490;

4. Hanna Kwon, Tobias E. Schrader, Andreas Ostermann, Matthew P. Blakeley,
Emma L. Raven & Peter C.E. Moody (2020) Heme peroxidase—Trapping
intermediates by cryo neutron crystallography Methods in Enzymology Vol 634
(Ed. P C E Moody)

5. H Kwon, PS Langan, L Coates, EL Raven & PCE Moody (2018) The rise of
neutron cryo-crystallography. Acta Cryst. D74, 792-799

6. H Kwon, O Smith, EL Raven & PCE Moody (2017) Combining X-ray and Neutron
Crystallography with Spectroscopy. Acta Cryst D72 141- 147

7. DD Turner, L Lad, H Kwon, J Basran, KH Carr, PCE Moody & EL Raven (2017)
The role of Ala134 in controlling substrate binding and reactivity in
ascorbate peroxidase J. Inorg. Biochem. Volume 180, March 2018, Pages
230-234 8. PCE Moody & EL Raven (2018) The Nature & Reactivity of Ferryl
Heme in Compounds I and II Acc. Chem Res. 51, 2, 427–435

8. PCE Moody & EL Raven (2018) The Nature & Reactivity of Ferryl Heme in
Compounds I and II Acc. Chem Res. 51, 2, 427–435



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[ccp4bb] clips for unipucks

[Peter Moody]

Hello,
has anyone in the UK a source for the little (~5 mm) clips that go on the
side of  unipucks? Molecular Dimensions don't get back to me..I could order
from the USA, but it is a lot of bother and I'm too stingy to pay silly
shipping costs...I only need one, but more than happy to buy a few if need
be.

Peter



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[ccp4bb] Neutron macromolecular crystallography in the UK - A new facility

[Peter Moody]

*ISIS Endeavor User Meeting   *
*Thursday 8 July, 1.30pm BST*

Your chance to hear (and shape)  the case for having a state of the art
instrument for large unit cell (protein) neutron crystallography at ISIS on
the Diamond / Harwell campus. As well as other biological/medical
facilities like SANS and reflectometry.

Please join the meeting, the link to register is on the meeting home page
https://www.isis.stfc.ac.uk/Pages/News21_EndeavourMeetings.aspx

Are you fed up with seeing only half of your atoms? Come along!

Peter
Please do not reply to me using this email address, I might miss it. If you
want to get in touch use my Leicester email.



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[ccp4bb] Lectureship at Leicester (LISCB)!

[Peter Moody]

We have just posted an advertisement for a lecturer in structural biology
at Leicester Institute for Structural and Chemical Biology.

Closing date for applications 22 April

see https://jobs.le.ac.uk/vacancies/2983/lecturer-in-structural-biology.html

for more information.


We would love to hear from you.
Peter

Please don't reply to this email, emails to my leicester.ac.uk email
address are much more likely to be noticed.



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[ccp4bb] Post-doc in CryoEM at Scripps Florida

[Peter Moody]

Dear All,


Scripps Florida have a brand  new Jeol CryoARM300, the first between
Glasgow and the Pacific Ocean (going west).

 Dr Izard has a Post-doc position available to use it.  This would be
especially attractive for someone interested in cell adhesion and who hates
cold dark winters


 see



https://jobs.sciencecareers.org/job/525517/postdoctoral-associate-in-cryogenic-electron-microscopy-cryoem-/?LinkSource=PremiumListing



Please send enquires directly to Dr Izard, 



best wishes, Peter


NB I don't monitor this account as often as I should, so if seeing this
message prompts you to say "hello" please use my Leicester email.



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Re: [ccp4bb] Issues in new Mac version 10.15

[Peter Moody]

Xquartz reinstall works for me, but the CCP4 updater is broken.
At the "Applying changes" step it will seem to pause (although using 100%
of a cpu) and will continue to run despite exiting.
Forced quit is needed (but doesn't seem to do any harm).

Peter
( I am very bad at monitoring this account, please use my university email
address if you want to contact me directly)

On Thu, 17 Oct 2019 at 09:24, Charles Ballard - UKRI STFC <
charles.ball...@stfc.ac.uk> wrote:

> Dear All
>
> as has been pointed out, and as per usual, OS X updates seem to remove
> some of the setup for XQuartz, which will cause most X11 based apps to stop
> working.  It is best to re-install XQuartz.  This will work for an updated
> system that had CCP4 previously installed on it.  We have had a few reports
> of issues when installing on a fresh  10.15 machine through the CCP4
> downloads manager (tarball route still works).  We are investigating.
>
> All the best
>
> Charles
>
> On 16 Oct 2019, at 17:42, Werther, Rachel A wrote:
>
> Thanks to all who gave advice.  The reinstallation of XQuartz worked for
> me.  I was using the most updated version of XQuartz before I reinstalled
> it, but as Guillaume Gaullier told me:
>
> “…macOS updates typically wipe out most files of your XQuartz installation
> (XQuartz.app will still be where it was originally installed, but unlike
> most Mac applications this one is not self-contained and has important
> files under /opt/X11 that get erased by a system update). And Coot requires
> XQuartz to display its window, so this is the most likely explanation for
> why it would not work after a system update.
>
> Try reinstalling XQuartz from https://www.xquartz.org/<
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.xquartz.org_=DwMFaQ=eRAMFD45gAfqt84VtBcfhQ=DO9lvOAiEYffd0DHXxXRFRhnm_KEyAdWVXbYX9zO5B8=zb3XqXe1iBKaPGEDyfZCe-uLxGJJVI0SzgY3of7iAxk=3FyzcByzIrl83gOdCoaiFSzE7Mbhtist6uxzCuQjIXA=>,
> then log out and log back in (or reboot, that should do it too), and see if
> Coot starts up normally.”
>
> Happy solving,
> Rachel
>
> Rachel Werther / Research Technician III / Stoddard Lab / Basic Sciences /
> Fred Hutchinson Cancer Research Center / rwert...@fredhutch.org rwert...@fredhutch.org> / 206-667-4066
>
> From: CCP4 bulletin board  CCP4BB@JISCMAIL.AC.UK>> on behalf of "Werther, Rachel A" <
> rwert...@fredhutch.org>
> Reply-To: "Werther, Rachel A"  rwert...@fredhutch.org>>
> Date: Tuesday, October 15, 2019 at 5:01 PM
> To: "CCP4BB@JISCMAIL.AC.UK" <
> CCP4BB@JISCMAIL.AC.UK>
> Subject: [ccp4bb] Issues in new Mac version 10.15
>
> Hello All,
>
> I downloaded the latest Mac Update, 10.15 Catalina, and then Coot wouldn’t
> open on my computer.
>
> Phenix opened as usual.  I use the GUI, and the button that says “Open in
> COOT” was not greyed out, but would not launch the window.  When I tried to
> open it directly from Finder, it also failed to open.  The cartoon coot
> appeared on my recently opened section of my bottom-of-screen toolbar, but
> nothing happened.
>
> Next I downloaded the latest CCP4-7.0.077, and followed the instructions
> to remove the extended attributes:
> ATTENTION: If you are planning to install CCP4 from a tarball on Mac OS X
> version 10.13 or later (10.12 was not tested), you will have to remove
> extended attributes from the tar-gz-file before unpacking it, otherwise the
> app icons will not be functional (and you will be able to launch the CCP4
> apps including ccp4i and ccp4i2 from the command line only). The extended
> attributes can be removed from the file _file_ using the command "xattr -c
> _file_". For example: xattr -c ccp4-7.0.065-macosx64.tar.gz
>
> But when I try to open CCP4, I get this message:
> Ccp4 cannot be opened because of a problem.
> Check with the developer to make sure ccp4 works with this version of
> macOS. You may need to reinstall the application. Be sure to install any
> available updates for the application and macOS.
> Click Report to see more detailed information and send a report to Apple.
>
> And when I try to open Coot from the Finder, I again just see the icon in
> my recently opened section of my bottom-of-screen toolbar, but it doesn’t
> open.
>
> Any advice?
>
> Many thanks,
> Rachel
>
> Rachel Werther / Research Technician III / Stoddard Lab / Basic Sciences /
> Fred Hutchinson Cancer Research Center / rwert...@fredhutch.org rwert...@fredhutch.org> / 206-667-4066
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1<
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMGaQ=eRAMFD45gAfqt84VtBcfhQ=DO9lvOAiEYffd0DHXxXRFRhnm_KEyAdWVXbYX9zO5B8=DLlHXm0LUKHS_PFqce1iCejwGvyoaCkFpJGwuJyob_Q=HfIn8TsXm95kj-mZzZ_fHbCh2I6Lzu3-v2XlHisInZQ=
> >
>
> 

[ccp4bb] Home/EU PhD studentship at Leicester

[Peter Moody]

I have funding to cover the stipend and fees for up to 4 years for a PhD
student, funded by the Royal Society.

I should be most grateful if you could tell your brightest and best
students. I am particularly keen recruit someone who wants to explore new
(and not so new)  and exciting ways to look at the way enzymes work.
Imagination and curiosity will be needed.

The link is on FindAPhD
https://www.findaphd.com/phds/project/enzyme-mechanism-through-advanced-techniques/?p109342
<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.findaphd.com%2Fphds%2Fproject%2Fenzyme-mechanism-through-advanced-techniques%2F%3Fp109342=02%7C01%7Cpcem1%40leicester.ac.uk%7C72a16d2d6ad746d6070f08d6cfb9cc38%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C636924794227787136=MgeMTkKxWZwYqQDXiFO25EGUvJdNhRJAlwPmaLrAVOA%3D=0>

Please don't reply to this email address, use peter.moody at le.ac.uk

Peter Moody
Leicester Institute for Structural and Chemical Biology



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[ccp4bb] MRC-IMPaCT PhD -LISCB Leicester & MPL Diamond

[Peter Moody]

*Deadline Sunday 20 January 2019*.

The theme for the MRC IMPaCT programme is complex disease.  This project
studies membrane protein complexes relevant to fibrosis, and funding is for
3.5 years. It will be based within LISCB (Leicester Institute for
Structural & Chemical Biology), and is a partnership with NIHR Leicester
BRC-Respiratory, and the Membrane Protein Lab at Diamond/Harwell.
Prospective applicants are encouraged contact *Bibek Gooptu*

/Andrew Quigley to discuss and can access the application form via this
link (one among various listed projects):

https://more.bham.ac.uk/mrc-impact/phd-opportunities/
Converting insult into injury: Cellular and structural biology studies of a
macromolecular complex that links inflammation with scarring in fibrotic
disease

Supervisors: Bibek Gooptu (UoL) and and Andrew Quigley (Diamond)

45% of deaths in the developed world arise as a result of fibrosis –
replacement of normal tissue with scar. Fibrosis is a basic response to
severe or sustained insult. If confined, fibrosis can limit further tissue
damage, but when widespread it leads to organ failure, cancer risk, and
death. We study how different insults cause fibrosis, focusing on lung and
liver disease. We have recently identified a molecular complex that
represents a junction between acute inflammation and chronic scarring
pathways, and may be an important target for future drug therapies. This
project will use state-of-the-art cellular and structural biology
approaches to understand the molecular details of how the complex
assembles, works, and may be targeted by drugs. It will be studied in the
context of intracellular (glycoprotein misfolding) and extracellular
(bacterial molecule) insults. The work is excitingly cross-disciplinary
(membrane protein crystallography, cryo-EM, cell biology, and integration
within clinical/translational studies). It is also cross-institutional
(Leicester Institute of Structural and Chemical Biology, NIHR Leicester
BRC, Research Complex at Harwell, Diamond Light Source). The supervisors
span these institutions and areas of expertise, from clinical to atomic
resolution studies, and can offer outstanding training and support.


Posted on behalf of *Bibek Gooptu **Professor of Respiratory Biology, LISCB
and NIHR BRC-Respiratory, University of Leicester*

* Consultant in Respiratory Medicine, Glenfield Hospital*

*Please do not reply to me, I'm not very good at looking after this account
-Peter*



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Re: [ccp4bb] PDRA Position, Leicester, with Peter Moody

[Peter Moody]

PS closing date is October 27th, please only apply through the  link  at
https://www.jobs.ac.uk/job/BND638/postdoctoral-research-associate
Thanks, Peter

On Fri, 28 Sep 2018 at 18:17, Peter Moody  wrote:

> I have a BBSRC-funded PDRA position for someone to come and work with me
> at the Leicester Institute for Structural & Chemical Biology, and so  this
> is about to be posted on jobs.ac.uk.   Please contact me using my
> university email, and not through this account (as the message will
> probaly get lost).
> Vacancy Name: Postdoctoral Research Associate
> Vacancy ID: 474
> Vacancy Department: Leicester Institute of Structural and Chemical
> Biology/Molecular and Cell Biology
> Advertising Start Date: 28/09/2018 00:00:00
> Advertised Salary: Grade 7 £34,189 to £39,609 per annum
>
>
> We wish to recruit a Postdoctoral Researcher to the group of Prof Peter
> Moody to take a leading role in a programme of research to investigate the
> mechanism of heme peroxidases, using advanced and innovative structural
> and spectroscopic methods. Our work is summarised in Moody & Raven (2018) 
> *Acc.Chem.
> Res.* 51 (2), pp 427–435 *DOI: *10.1021/acs.accounts.7b00463, and in more
> detail in the papers listed on Peter Moody’s Departmental home page https
> ://www2.le.ac.uk/departments/molcellbiol/staff/moody
> <https://www2.le.ac.uk/departments/molcellbiol/staff/moody>
>
> The research is funded by the BBSRC and is a collaboration with Professor
> Emma Raven of the Chemistry Department at Bristol University (http://www.
> bris.ac.uk/chemistry/people/emma-raven/index.html) and will involve
> expressing and purifying proteins from recombinant sources, gaining s
> tructural and mechanistic insights using X-ray (using home and
> synchrotron sources) and Neutron crystallography (using ILL Grenoble, FRM-II
> Munich and ONRL, USA). We have recently conducted experiments using the
> Free Electron Laser SACLA in Japan and hope to use other FEL sources such
> as EuXFEL soon. Leicester has recently acquired state of the art cryo-electron
> microscopes and we would like to explore the potential for micro electron
> diffraction. A wide range of biochemical and biophysical techniques
> (especially spectroscopy) will be used to explore enzyme intermediates.
>
> You will  develop your own original research projects, in line with the
> aims and objectives of the research programme and assist with the
> supervision of graduate and undergraduate students. You will write up your
> research findings for dissemination amongst the research team and the
> broader international community and make presentations at scientific
> meetings in the UK and overseas.
> About you
>
> The successful applicant should hold a PhD, have a strong background in
> biochemical or structural analysis of proteins and have a keen interest in
> experimental design and determining the direction of the research programme.
>
> Additional information
>
> LISCB comprises over 20 research groups drawn from several departments,
> including the Department of Molecular and Cell Biology, and brings together
> internationally renowned research using structural biology, chemical
> biology and single molecule methods to investigate major challenges in
> fundamental biological processes into a single world-leading unit.
>
> The University of Leicester is committed to international excellence,
> world-changing research and high quality, inspirational teaching. Recently,
> the MRC in partnership with the Universities of Leicester, Warwick,
> Nottingham and Birmingham has invested into a state-of-the-art CryoEM
> facility at the Leicester Institute for Structural and Chemical Biology (
> LISCB), one of four new, flagship Research Institutes of the University
> of Leicester. We are strongly committed to inclusivity, promoting
> equality and celebrating diversity among our staff and students. You will
> develop your career in a supportive and collaborative academic
> environment in one of the world’s leading research-intensive
> universities; elite in the excellence of our research, yet distinctive for
> the genuine synergy between our research and teaching.
> In return for your hard work, we offer a working environment that is
> committed to inclusivity, through promoting equality and valuing
> diversity. We offer a salary package with excellent pension scheme, a
> generous annual leave allowance and an online portal that offers a range of
> lifestyle benefits and discounts. Located close to Leicester city centre,
> our award winning campus benefits from a wide range of cafes, a fully
> equipped sports centre and nursery facilities. Further information
> regarding our extensive range of

[ccp4bb] PDRA Position, Leicester, with Peter Moody

[Peter Moody]

I have a BBSRC-funded PDRA position for someone to come and work with me at
the Leicester Institute for Structural & Chemical Biology, and so  this is
about to be posted on jobs.ac.uk.   Please contact me using my university
email, and not through this account (as the message will probaly get lost).
Vacancy Name: Postdoctoral Research Associate
Vacancy ID: 474
Vacancy Department: Leicester Institute of Structural and Chemical
Biology/Molecular and Cell Biology
Advertising Start Date: 28/09/2018 00:00:00
Advertised Salary: Grade 7 £34,189 to £39,609 per annum


We wish to recruit a Postdoctoral Researcher to the group of Prof Peter
Moody to take a leading role in a programme of research to investigate the
mechanism of heme peroxidases, using advanced and innovative structural and
spectroscopic methods. Our work is summarised in Moody & Raven (2018)
*Acc.Chem.
Res.* 51 (2), pp 427–435 *DOI: *10.1021/acs.accounts.7b00463, and in more
detail in the papers listed on Peter Moody’s Departmental home page https
://www2.le.ac.uk/departments/molcellbiol/staff/moody
<https://www2.le.ac.uk/departments/molcellbiol/staff/moody>

The research is funded by the BBSRC and is a collaboration with Professor
Emma Raven of the Chemistry Department at Bristol University (http://www.
bris.ac.uk/chemistry/people/emma-raven/index.html) and will involve
expressing and purifying proteins from recombinant sources, gaining s
tructural and mechanistic insights using X-ray (using home and synchrotron
sources) and Neutron crystallography (using ILL Grenoble, FRM-II Munich and
ONRL, USA). We have recently conducted experiments using the Free Electron
Laser SACLA in Japan and hope to use other FEL sources such as EuXFEL soon.
Leicester has recently acquired state of the art cryo-electron microscopes
and we would like to explore the potential for micro electron diffraction.
A wide range of biochemical and biophysical techniques (especially
spectroscopy) will be used to explore enzyme intermediates.

You will  develop your own original research projects, in line with the
aims and objectives of the research programme and assist with the
supervision of graduate and undergraduate students. You will write up your
research findings for dissemination amongst the research team and the
broader international community and make presentations at scientific
meetings in the UK and overseas.
About you

The successful applicant should hold a PhD, have a strong background in
biochemical or structural analysis of proteins and have a keen interest in
experimental design and determining the direction of the research programme.

Additional information

LISCB comprises over 20 research groups drawn from several departments,
including the Department of Molecular and Cell Biology, and brings together
internationally renowned research using structural biology, chemical
biology and single molecule methods to investigate major challenges in
fundamental biological processes into a single world-leading unit.

The University of Leicester is committed to international excellence,
world-changing research and high quality, inspirational teaching. Recently,
the MRC in partnership with the Universities of Leicester, Warwick,
Nottingham and Birmingham has invested into a state-of-the-art CryoEM
facility at the Leicester Institute for Structural and Chemical Biology (
LISCB), one of four new, flagship Research Institutes of the University of
Leicester. We are strongly committed to inclusivity, promoting equality and
celebrating diversity among our staff and students. You will develop your
career in a supportive and collaborative academic environment in one of the
world’s leading research-intensive universities; elite in the excellence of
our research, yet distinctive for the genuine synergy between our research
and teaching.
In return for your hard work, we offer a working environment that is
committed to inclusivity, through promoting equality and valuing diversity.
We offer a salary package with excellent pension scheme, a generous annual
leave allowance and an online portal that offers a range of lifestyle
benefits and discounts. Located close to Leicester city centre, our award
winning campus benefits from a wide range of cafes, a fully equipped sports
centre and nursery facilities. Further information regarding our extensive
range of staff benefits is available here.
<https://www2.le.ac.uk/staff/working/staff-benefits>


Informal enquiries and are welcome and should be made to Professor Peter
Moody on Tel: +44 (0)116 229 7097 or email: peter.mo...@leicester.ac.uk




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Cartesian/Harvard/Digilab Honeybee 8+1

[Peter Moody]

We are retiring our Cartesian Honeybee 8+1 crystallisation robot and need
the space, if anyone has a use for it (some of the parts are quite
difficult to get hold of now and/or are quite expensive) please get in
touch.   Price is £GB 0.00 but buyer collects.

Please contact me directly using my University of Leicester email
(discoverable with all good search engines) as I don't pay as much
attention to this account as I should.

Peter Moody
Leicester Institute for Structural and Molecular Biology



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Academic (Chair and Lecturships) and Research Posts available at Leicester Institute!

[Peter Moody]

We have established the "Leicester Institute of Structural & Chemical
Biology" at the University of Leicester, and have new positions, that is
1* Chair*,
3 *Lectureships in Chemical Biology*
1 *Lectureship  in Structural Biology*,
2* Research Fellowships* ("For promising researchers making the transition
to independence. This scheme is aligned with the Wellcome Trust
Institutional Strategic Support Fund".)
2 *research posts developing NMR* tools and software (CCPN),
2 *research posts* on the control of gene expression by *Histone Deactylase
complexes*.

If you would care to join us in this wonderful adventure (I'm tempted to
say become institutionalised), then please look at
https://www2.le.ac.uk/institutes/liscb/work-at-liscb for further details.
Please come, we need your lovely brains.  Note closing date is 24 April


Peter (please send enquiries to our Manager, Dr Peter Watson via email (
peterwat...@le.ac.uk) or by telephone (0116 373 6436), *not* by replying to
this email)

[ccp4bb] PhD UCL/National Institute of Biological Standards and Control (NIBSC)

[Peter Moody]

The very excellent Dr Clive Metcalfe (an ex-post-doc with me) of NIBSC has
a PhD project with Prof Paul Dalby at UCL looking at disulphide bond
reduction in monoclonal antibodies.
 If you have a good student who might be interested please point them to
https://www.prism.ucl.ac.uk/#!/?project=205

Peter

[ccp4bb] PhD studentships at Universiy of Leicester

[Peter Moody]

The newly founded (and exceptionally wonderful)  Leicester Institute for
Structural & Chemical Biology has funded PhD studentships available for
September 2017 start

Please see

http://www2.le.ac.uk/institutes/liscb/study-at-liscb





We also members of
the *M*idlands *I*ntegrative *B*iosciences* P*artnership, the home page is

http://www2.warwick.ac.uk/fac/cross_fac/mibtp/


Suitably brilliant candiates with an addiction to high-risk and wish for
obscurity might like to look at
http://www2.warwick.ac.uk/fac/cross_fac/mibtp/pgstudy/phd_opportunities/molecular2017/neutron




Compliments of the season, Peter


PS please do not reply to this email address, the popularity of CCP4BB
means thing get lost.

Re: [ccp4bb] Trump

[Peter Moody]

I don't think I want to be friends with anyone who approves of racism,
misogyny and xenophobia

On 9 November 2016 at 18:32, Gert Vriend 
wrote:

> Lets stop this discussion before it divides this list of friends just as
> much as the cause of this discussion divided the US.
>
> Gert
>

Re: [ccp4bb] proton scattering by X-rays

[Peter Moody]

Thank you all for explaining, I'm glad it was my pedantic lack of ability
to get over the description and think of the chemistry that was the
problem. Of course the positive charge would not be localised just on the
hydrogen, it is not really just a proton and so  it will have some electron
density.

Peter

On 2 February 2015 at 13:08, Peter Moody pcem1bigfi...@gmail.com wrote:

 Dear BB


 I have (again) realised how limited by understanding of our subject is.


 In Nature’s online site
 http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14110.html?WT.ec_id=NATURE-20150129
 there is a paper describing an X-ray structure determined with sub-atomic
 data (nice!).  The figures show density for H+ as well as H-. In my
 simple way I had assumed that any X-ray scattering from the nucleus was
 negligible, and that the electrons are responsible for this. I would expect
 a proton (i.e. H+) alone to be invisible to X-rays, and certainly not to
 look similar to a hydride (with two electrons in (electron density) maps.
 What have I missed?  Could someone please explain, or point me to a
 suitable reference?


 Best wishes, Peter

 (please use peter.mo...@le.ac.uk to reply directly)

 http://www2.le.ac.uk/departments/biochemistry/staff/moody

[ccp4bb] proton scattering by X-rays

[Peter Moody]

Dear BB


I have (again) realised how limited by understanding of our subject is.


In Nature’s online site
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14110.html?WT.ec_id=NATURE-20150129
there is a paper describing an X-ray structure determined with sub-atomic
data (nice!).  The figures show density for H+ as well as H-. In my simple
way I had assumed that any X-ray scattering from the nucleus was
negligible, and that the electrons are responsible for this. I would expect
a proton (i.e. H+) alone to be invisible to X-rays, and certainly not to
look similar to a hydride (with two electrons in (electron density) maps.
What have I missed?  Could someone please explain, or point me to a
suitable reference?


Best wishes, Peter

(please use peter.mo...@le.ac.uk to reply directly)

http://www2.le.ac.uk/departments/biochemistry/staff/moody

[ccp4bb] someone noticed !

[Peter Moody]

http://www.theguardian.com/commentisfree/2014/jan/02/in-praise-of-crystallography-editorial

P

[ccp4bb] BBSRC- funded PDRA post on heme enzymes at Leicester

[Peter Moody]

The project will involve structural, functional and mechanistic studies on
different heme proteins, including neutron crystallography and single
crystal resonance Raman spectroscopy. This work is a collaboration of
Peter Moody in the Department of Biochemistry and  Emma Raven in the
Department of Chemistry (but we are in the same building).

The link is
http://ig5.i-grasp.com/fe/tpl_UniversityOfLeicester01.asp?s=4A515F4E5A565B1Ajobid=82300,2348228658key=78315784c=786021238234pagestamp=sevlztwcyjtrujnidq


Informal enquiries are welcome, but please use my universiy email (
peter.mo...@le.ac.uk) not this one.

Peter Moody
1/56 Henry Wellcome Laboratories
University of Leicester
Lancaster Road
Leicester
LE1 9HN
UK
tel. (0)116 229 7097


http://www2.le.ac.uk/departments/biochemistry/staff/moodyredir.aspx?C=7h19pcspqEmPAALvHREjMjo_krJWbNBI_LMEQufsD8fcXnwT9NTTIL6o7-nOe5BjK9EY1boVZ6U.URL=http%3a%2f%2fwww2.le.ac.uk%2fdepartments%2fbiochemistry%2fstaff%2fmoody

[ccp4bb] OT: (a bit) shelx(pro)

[Peter Moody]

At the risk of (more) people pointing at me and laughing...

I used to use SHELXPRO to get my .ins files sorted for SHELX, but that
seems to have gone.

How is it done now?

I want to do a full-matrix refinement to get ESUs on some (specific) atoms
and as far as I can remember SHELXL is the best way to go.

Any advice gratefully received, if its RTFM, then a refernce/link to th
right page would be nice.

best wishes, Peter

Re: [ccp4bb] Crystallisation below 0°C

[Peter Moody]

If your precipitant is high concentration salt, there will be a significant
freezing point depression (see e.g. wikipedia entry
http://en.wikipedia.org/wiki/Freezing-point_depression ).  I seem to
remember collecting data from crystals we cooled to -15 C in the early
'80s. The crystals were grown in 2.4M Ammonium sulphate and harvested into
2.8M. Its true they were grown at room temperature but this would suggest
there is no reason crystals could not be grown from high salt
concentrations between 0 and whatever freezing point your precipitant
solution has.
Peter



On 30 May 2013 15:25, Matthew Franklin mfrank...@nysbc.org wrote:

  Hi Glenn -

 I have nothing systematic, but I remember that transducin-alpha (1TND) was
 crystallized at -12 C, with 20% glycerol in the mother liquor.  (The
 crystals grew at higher temperatures, but weren't as good.)  I worked on
 this project briefly in grad school, and I remember that looking at the
 crystals was a big nuisance - you had to take the trays out of the -12
 freezer, run to the cold room, and look at them quickly before they warmed
 up too much!

 - Matt



 On 5/30/13 7:26 AM, Glenn Masson wrote:

 Hello CCP4BBers,

  I am currently playing with some crystals that seem to enjoy lower
 temperatures, and I was thinking of breaking the 0°C threshold.

  Looking for examples of this in the literature is problematic, as
 searching for examples in the PDB (Under the advanced search- crystal
 properties- temperature (K)) turns up a large amount of false positives.
 Many otherwise supremely intelligent people seem unable or unwilling to
 grasp the concept of Kelvin (it's amazing how many protein structures were
 solved only 22 degrees above absolute zero...).

  I was wondering if anyone has much experience in this area? I see a few
 structures e.g. 2Z97 (-5°C) and 4H0W (-2°C), but I was wondering if anyone
 has a more systematic knowledge, some more examples, and what the
 parameters and best practice of this technique are.

  Many thanks,

  Glenn Masson

 MRC-Laboratory of Molecular Biology



 --
 Matthew Franklin, Ph. D.
 Senior Scientist
 New York Structural Biology Center
 89 Convent Avenue, New York, NY 10027(212) 939-0660 ext. 9374

Re: [ccp4bb] Struther Arnott

[Peter Moody]

Sad news indeed, he mentored my mentors,   His influence on crystallography
(rather than fibre diffraction) in not always as well appreciated as it
might be.

Peter


On 22 April 2013 14:44, James Naismith naism...@st-andrews.ac.uk wrote:

 Older members of the bulletin board will be sad to learn that Struther
 Arnott FRS, fibre diffractionist and biophysicist (as well as former St
 Andrews Principal) died on Saturday.

 Jim Naismith


 James H. Naismith FRSE FMedSci| naism...@st-andrews.ac.uk
 Professor of Chemical Biology   | j...@st-andrews.ac.uk (teaching)
 BSRC  |
 The North Haugh   |+44(0)1334463792
 The University, St Andrews|Secretary: +44(0)1334463401
 Fife KY16 9ST U.K.   |Fax: (44) or (0) 1334467229

 Google scholar is free and tracks your outputs, mine are
 http://scholar.google.co.uk/citations?hl=enuser=fLmKKQMJ

 The University of St Andrews is a charity registered in Scotland : No
 SC013532

[ccp4bb] OT: Funded PhD at University of Leicester, UK and Institut Laue-Langevin Grenoble, France

[Peter Moody]

I should be most grateful if you could point your most able students who
might be considering a PhD to one of the following links.


http://www2.le.ac.uk/departments/biochemistry/postgraduate-study/Three-year%20PhD%20programme.doc

or

http://www2.le.ac.uk/departments/chemistry/people/academic-staff/professor-emma-raven

This is an exciting project  looking at electron transfer and domain
movements. There is good stipend,  and the student will get  to use old
soviet nuclear weapons without killing anyone.

I believe the student must be a resident of the EU.

best wishes, Peter

Keywords: SANS, neutron reflectometry, EPR, kinetics, optical spectroscopy,
cytochrome P450 reductase, redox enzymes, heme.

Re: [ccp4bb] first use of synchrotron radiation in PX

[Peter Moody]

When I started my PhD (in 1980!) at Imperial, David Blow already had a PhD
student who's project was to use the new Daresbury synchrotron to exploit
anomalous differences. Unfortunately it didn't  come on line in time for
him to actually get the data he needed.
I'd be intrigued to know who got the first structure from Daresbury. I
don't remember feeling there was a race at the time, but then we were a lot
less competitive in those days!
Peter

On 13 March 2013 16:21, Colin Nave colin.n...@diamond.ac.uk wrote:

 Yes, this is a key paper demonstrating the possibilities.

 The answer to the question of first structure solved is a bit more
 difficult. Much of the early use of synchrotrons was for collecting high
 resolution data for refinement to supplement data collected on lab sources.
 This included data from similar structures with more or less sequence
 identity as well as data from heavy atom derivatives. MAD structures
 appeared somewhat later (see the references in Proc. Nati. Acad. Sci. USA
 Vol. 86, pp. 2190-2194, April 1989 for some early examples).

 Of course John Helliwell's book (Macromolecular Crystallography with
 Synchrotron Radiation, chapter 10) gives a useful historical introduction.

 Other than the above, if anyone has a claim to first structure solved just
 with synchrotron radiation then they should speak up!

 Colin

 -Original Message-
 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
 Harry Powell
 Sent: 13 March 2013 15:04
 To: ccp4bb
 Subject: Re: [ccp4bb] first use of synchrotron radiation in PX

 Hi

 Not sure if this is strictly speaking the first protein *solved* on a
 synchrotron, but I think this is the first report of shooting protein
 crystals at a synchrotron in the widely available literature -

 http://www.pnas.org/content/73/1/128.full.pdf+html

 Phillips J C, Wlodawer A, Yevitz M M and Hodgson K 0 1976 Proc.
 Nat. Acad. Sci. USA 73 128-32

 Applications of synchrotron radiation to protein crystallography:
 Preliminary results


 On 13 Mar 2013, at 14:38, Alan Cheung wrote:

  Hi all - i'm sure this many will know this : when and what was the first
 protein structure solved on a synchrotron?
 
  Thanks in advance
  Alan
 
 
  --
  Alan Cheung
  Gene Center
  Ludwig-Maximilians-University
  Feodor-Lynen-Str. 25
  81377 Munich
  Germany
  Phone:  +49-89-2180-76845
  Fax:  +49-89-2180-76999
  E-mail: che...@lmb.uni-muenchen.de

 Harry
 --
 Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick
 Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of European
 Crystallographic Association SIG9 (Crystallographic Computing)



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Re: [ccp4bb] Etiquette on publishing if there is a crystallization report from someone else.

[Peter Moody]

Its not always the case that the project has been abandoned or died, some
labs will push crystallisation notes to give a student paper-writing
experience, and could have invested a significant effort since in the
project. They could be waiting for e.g. the complex that makes it
interesting. Or the PI could be slow and inefficient (like me)!

If its a simple MR task, and the other groups crystals are the same as
yours, then its perhaps  unlikely they would not have solved it.

In the old days the thing to do would be to contact the other group and see
what their plans are. But this requires people to be nice to each other,
and I'm not sure that works anymore, even in crystallography.

Peter


On 25 September 2012 15:03, Nat Echols nathaniel.ech...@gmail.com wrote:

 On Tue, Sep 25, 2012 at 6:51 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de
 wrote:
  I would assume that someone who publishes crystallisation conditions has
  given up solving the structure or some other reason to encourage others
  to pick up the project, i.e., no, I don't see much point NOT
  publishing your data.

 I always assumed that the point of publishing crystallization
 conditions was to establish priority, and apparently there was once
 such an unspoken rule about publishing the structure.  Or so I'm told;
 from what I've seen it's long abandoned.

 A bit of historical perspective (about a very high-profile project):

 http://www.sciencemag.org/content/285/5436/2048.full

 -Nat

Re: [ccp4bb] space group and multiplicity

[Peter Moody]

I don't want to confuse things further, but as a PS to Ian's answer that
clearly tells you how to get Z..

You should be aware that a crystal might also have non-crystallographic
symmetry.

 Ian's answer  is right for Z, but as you also mentioned monomers I thought
I should mention that if the a.u. comprises a multimer then you would have
to multiply.

i.e. symops will give the number of copies of the asymmetric unit in the
unit cell, this might not be the number of monomers.

Peter



On 2 August 2012 10:12, Ian Tickle ianj...@gmail.com wrote:

 Hi Careina

 The obvious answer is to look it up in International Tables vol. A.
 If you don't have access to that you can look up the text file
 $CLIBD/syminfo.lib in the CCP4 distribution and work it out from
 there.  Fpr a given space group you need to count the number of
 'symop' lines.  That's the number of asymmetric units in the primitive
 cell.  If you want the number in a centred cell, also count the number
 of 'cenop' lines: that's the number of centring translations, so to
 get the total no of a.u.'s in the centred cell you would multiply
 these two numbers.

 I'm afraid there isn't an easier way, for example you can't get it
 straightforwardly from the space group symbol.

 HTH

 -- Ian

 On 2 August 2012 09:37, Careina Edgooms careinaedgo...@yahoo.com wrote:
  Dear ccp4
 
  I ask a very fundamental question because I have not had formal training
 in
  this and I would like to understand.
  How can I obtain the multiplicity (z) from the space group? So for
 example
  if the space group is P222 how do I know that there are 4 monomers in the
  unit cell? Or if it is P422 then there is 8? I am only concerning myself
  with a primitive lattice for now because I am sure the others are more
  complicated.
  thanks
  Careina

Re: [ccp4bb] Iron induced reduction of crystal

[Peter Moody]

Take a look at  http://en.wikipedia.org/wiki/Great_Oxygenation_Event

This might suggest you may have used up the available oxygen.

If you would like to try growing your crystals in an oxygen-free
environment, we (in Leicester) have a glove box with a Douglas Instruments
Oryx 4 robot. I know its not exactly handy for Glasgow, but ..

On 1 August 2012 13:53, RHYS GRINTER r.grinte...@research.gla.ac.uk wrote:

 Hi All,

 I'm currently working of a protein with a ferredoxin protein with
 anIron-Sulphur cluster. I was harvesting some crystals the other day and a
 piece of my scalpel blade broke off and ended up in the well solution. I
 Sealed the well without noticing, the shard of iron oxidised and the
 crystals lost most of their red colour:

 Ordinary crystals:

 http://s1058.photobucket.com/albums/t401/__Rhys__/?action=viewcurrent=MBPR_Rodcluster2edit.png

 Crystals from Blade containing well:

 http://s1058.photobucket.com/albums/t401/__Rhys__/?action=viewcurrent=MBPR_Bleached.png

 My explanation for this (If someone has a different one that'd be great
 too)

 Is that the oxidation of the metallic iron the well, created reducing
 conditions in the chamber and reduced the iron-sulphur cluster (reduced
 ferredoxin is much less strongly coloured).
 Which got me to thinking...Could this be applied as a technique to create
 reducing conditions in protein crystallography, as the use of reducing
 agents isn't always practical.

 Cheers,

 Rhys Grinter
 PhD Candidate
 University of Glasgow

[ccp4bb] Summary Re: anyone scrapping an Raxis-IV?

[Peter Moody]

Thank you for all  your suggestions.

Rigaku have discovered that shorting a couple of the output leads together
means the new type can be used as a replacement for the old type.

I'm very happy to say that it works!

This is a similar solution to that suggested by Herman Schreuder.

Kevin Roberts pointed to  generally available replacements that required a
change in voltage

Others were kind enough to tip me of about machines due to be replaced. I'm
not sure I should identify them in public, but thank you anyway.

Peter


On 17 April 2012 09:58, Peter Moody pcem1bigfi...@gmail.com wrote:

 Is anyone about to re-cycle a Rigaku RAXIS-IV?
 One of the inverters that power the erase lamps in ours is smoking, and
 Rigaku have not been able to source a replacement for us, hence the
 message to the BB.

 Our machine was made in November 1996 and uses the type of inverter
 connected with four pairs of wires (Rigaku can source the more recent
 3-pair types).  I can give more detail, pictures etc. but would not want to
 clutter up your inboxes.

 This is not the first of these inverters to fail, so it would also be nice
 to find a source so we can keep going with it a while longer.
 By we of course  I mean I, as is the machine I  play with whilst more
 serious people collect data on our more modern system, I clarify this just
 in case anyone should think my colleagues here are also stuck in the 20th
 century



 Thanks, Peter

 Peter Moody
 Henry Wellcome Laboratories
 University of Leicester
 Lancaster Road
 Leicester
 LE1 9HN
 UK
 tel. +44 (0)116 229 7097


 http://www2.le.ac.uk/departments/biochemistry/staff/moodyhttp://redir.aspx?C=1a0a7175d81e495690bfd3f4b0e0afafURL=http%3a%2f%2fwww2.le.ac.uk%2fdepartments%2fbiochemistry%2fstaff%2fmoody

Re: [ccp4bb] Anaerobic glovebox crystal cryo-cooling

[Peter Moody]

We have a similar setup at Leicester, but its new enough not to have got
that far yet!

I'd be interested in any replies you get.

best wishes, Peter


On 24 April 2012 15:20, David Gallagher dt...@mrc-mbu.cam.ac.uk wrote:

  Hi all,

 I've been using a Belle technologies anaerobic glovebox with in built
 microscope and liquid nitrogen dewar port in an attempt to harvest and
 cryo-cool crystals in an oxygen free environment.

 I've been having some problems with icing and think this is most likely
 due to slow speed that it is possible to plunge loops into the liquid
 nitrogen.  I've been plunging loops straight into vials preloaded into an
 ESRF puck (with pusher).   This requires more care than what I would
 ordinarily do (i.e. plunging into bulk liquid nitrogen then and manouvering
 into a vial afterwards and then clipping said vial into a cane) and so
 takes longer - perhaps leading to icing.  The latter technique is not
 available as the glovebox set up means that the dewar can only be reached
 by my right hand - the microscope is in the way!

 Does anyone have any experience of a similar set up and if so have some
 advice as to how I can overcome this problem?

 Many thanks,

 Dave Gallagher


 --
 *David Gallagher *
 PhD Student

 MRC Mitochondrial Biology Unit
 Wellcome Trust / MRC Building
 Hills Road
 Cambridge
 CB2 0XY

 Email: dt...@mrc-mbu.cam.ac.uk
 Phone: 01223 252913

[ccp4bb] anyone scrapping an Raxis-IV?

[Peter Moody]

Is anyone about to re-cycle a Rigaku RAXIS-IV?
One of the inverters that power the erase lamps in ours is smoking, and
Rigaku have not been able to source a replacement for us, hence the message
to the BB.

Our machine was made in November 1996 and uses the type of inverter
connected with four pairs of wires (Rigaku can source the more recent
3-pair types).  I can give more detail, pictures etc. but would not want to
clutter up your inboxes.

This is not the first of these inverters to fail, so it would also be nice
to find a source so we can keep going with it a while longer.
By we of course  I mean I, as is the machine I  play with whilst more
serious people collect data on our more modern system, I clarify this just
in case anyone should think my colleagues here are also stuck in the 20th
century



Thanks, Peter

Peter Moody
Henry Wellcome Laboratories
University of Leicester
Lancaster Road
Leicester
LE1 9HN
UK
tel. +44 (0)116 229 7097


http://www2.le.ac.uk/departments/biochemistry/staff/moodyredir.aspx?C=1a0a7175d81e495690bfd3f4b0e0afafURL=http%3a%2f%2fwww2.le.ac.uk%2fdepartments%2fbiochemistry%2fstaff%2fmoody

Re: [ccp4bb] MAD

[Peter Moody]

Ian,
If you visit Isaac Newton's old home at Woolsthorpe (near here) you will
see a conflicting claim for location of the classic prism experiment. You
will also find an apple tree in the garden, but that is another story..

Peter

PS this is my special ccp4bb email account, it doesn't always get the
attention it deserves.

On 19 January 2012 17:50, Ian Tickle ianj...@gmail.com wrote:

 Perhaps I could chime in with a bit of history as I understand it.

 The term 'dispersion' in optics, as everyone who knows their history
 is aware of, refers to the classic experiment by Sir Isaac Newton at
 Trinity College here in Cambridge where he observed white light being
 split up ('dispersed') into its component colours by a prism.  This is
 of course due to the variation in refractive index of glass with
 wavelength, so then we arrive at the usual definition of optical
 dispersion as dn/dlambda, i.e. the first derivative of the refractive
 index with respect to the wavelength.

 Now the refractive index of an average crystal at around 1 Ang
 wavelength differs by about 1 part in a million from 1, however it can
 be determined by very careful and precise interferometric experiments.
  It's safe to say therefore that the dispersion of X-rays (anomalous
 or otherwise) has no measurable effect whatsoever as far as the
 average X-ray diffraction experiment (SAD, MAD or otherwise) is
 concerned.  The question then is how did the term 'anomalous
 dispersion' get to be applied to X-ray diffraction?  The answer is
 that it turns out that the equation ('Kramer-Kronig relationship')
 governing X-ray scattering is completely analogous to that governing
 optical dispersion, so it's legitimate to use the term 'dispersive'
 (meaning 'analogous to dispersion') for the real part of the
 wavelength-dependent component of the X-ray scattering factor, because
 the real part of the refractive index is what describes dispersion
 (the imaginary part in both cases describes absorption).

 So then from 'dispersive' to 'dispersion' to describe the wavelength
 dependence of X-ray scattering is only a short step, even though it
 only behaves _like_ dispersion in its dependence on wavelength.
 However having two different meanings for the same word can get
 confusing and clearly should be avoided if at all possible.

 So what does this have to do with the MAD acronym?  I think it stemmed
 from a visit by Wayne Hendrickson to Birkbeck in London some time
 around 1990: he was invited by Tom Blundell to give a lecture on his
 MAD experiments.  At that time Wayne called it multi-wavelength
 anomalous dispersion.  Tom pointed out that this was really a misnomer
 for the reasons I've elucidated above.  Wayne liked the MAD acronym
 and wanted to keep it so he needed a replacement term starting with D
 and diffraction was the obvious choice, and if you look at the
 literature from then on Wayne at least consistently called it
 multi-wavelength anomalous diffraction.

 Cheers

 -- Ian

 On 18 January 2012 18:23, Phil Jeffrey pjeff...@princeton.edu wrote:
  Can I be dogmatic about this ?
 
  Multiwavelength anomalous diffraction from Hendrickson (1991) Science
 Vol.
  254 no. 5028 pp. 51-58
 
  Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings
  http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html
 
  Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst.
  (1994). D50, 11-16
 
  etc.
 
 
  I don't see where the problem lies:
 
  a SAD experiment is a single wavelength experiment where you are using
 the
  anomalous/dispersive signals for phasing
 
  a MAD experiment is a multiple wavelength version of SAD.  Hopefully one
  picks an appropriate range of wavelengths for whatever complex case one
 has.
 
  One can have SAD and MAD datasets that exploit anomalous/dispersive
 signals
  from multiple difference sources.  This after all is one of the things
 that
  SHARP is particularly good at accommodating.
 
  If you're not using the anomalous/dispersive signals for phasing, you're
  collecting native data.  After all C,N,O,S etc all have a small anomalous
  signal at all wavelengths, and metalloproteins usually have even larger
  signals so the mere presence of a theoretical d difference does not
 make it
  a SAD dataset.  ALL datasets contain some anomalous/dispersive signals,
 most
  of the time way down in the noise.
 
  Phil Jeffrey
  Princeton
 
 
 
  On 1/18/12 12:48 PM, Francis E Reyes wrote:
 
 
  Using the terms 'MAD' and 'SAD' have always been confusing to me when
  considering more complex phasing cases.  What happens if you have
 intrinsic
  Zn's, collect a 3wvl experiment and then derivatize it with SeMet or a
 heavy
  atom?  Or the MAD+native scenario (SHARP) ?
 
  Instead of using MAD/SAD nomenclature I favor explicitly stating whether
  dispersive/anomalous/isomorphous differences (and what heavy atoms for
 each
  ) were used in phasing.   Aren't analyzing the differences (independent

Re: [ccp4bb] STFC consultation on advisory panels

[Peter Moody]

Frank,


I don't have a plan, but as the consultation seeks the views of the
community. I would urge those with views to write to to STFC expressing
them, and mention this to their friends/colleagues/students/PI.  Although I
suspect that the views of people from industry will have more weight  than
than those of provincial academics, a significant volume of responses
expressing the anxiety that we will be under-represented in the new
structures should(?) mean the plans are reconsidered.


Perhaps, as you seem to suggest, people might also like to make their views
public through the BB?  This might lessen the activation energy of  those
intending to write something to STFC.


Peter

On 24 September 2011 22:32, Peter Moody pcem1bigfi...@gmail.com wrote:

 Could I draw (especially) UK users of STFC facilities (such as Diamond) to
 the STFC's proposals and consultation?
 http://www.stfc.ac.uk/About+STFC/36187.aspx

 Please note the composition of the Science Board and the research interests
 of the members, and with this in mind consider the question of the future of
 advisory panels.

 Facility users might remember the recent Programmatic Review and need for
 our community to fully inform the STFC of the importance of our work.

 I worry that we will be under represented in future discussions about
 resources (by we I mean macromolecular crystallographers, but this applies
 to biological scientists and indeed anyone interested in things smaller than
 planets and larger than sub-atomic particles).

 The closing date for the consultation is 14 October


 best wishes,
 Peter Moody,
 Leicester


 (PS don't reply to me at this address, I don't always give it the attention
 it deserves!)

[ccp4bb] STFC consultation on advisory panels

[Peter Moody]

Could I draw (especially) UK users of STFC facilities (such as Diamond) to
the STFC's proposals and consultation?
http://www.stfc.ac.uk/About+STFC/36187.aspx

Please note the composition of the Science Board and the research interests
of the members, and with this in mind consider the question of the future of
advisory panels.

Facility users might remember the recent Programmatic Review and need for
our community to fully inform the STFC of the importance of our work.

I worry that we will be under represented in future discussions about
resources (by we I mean macromolecular crystallographers, but this applies
to biological scientists and indeed anyone interested in things smaller than
planets and larger than sub-atomic particles).

The closing date for the consultation is 14 October


best wishes,
Peter Moody,
Leicester


(PS don't reply to me at this address, I don't always give it the attention
it deserves!)

[ccp4bb] William Nunn Lipscomb Jr The Colonel

[Peter Moody]

Nobel Laureate William Lipscomb Dies at 91
By THE ASSOCIATED PRESS
Published: April 15, 2011 at 2:01 PM ET

I have had this forwarded to me,  besides getting a Nobel prize for his
discovery of the bent bonds in boron hydrides, the Colonel was a pioneer in
PX, with work on the role of Zn in carboxypeptidase and the allosteric
mechanism of ATCase perhaps being the best known.  Peter



BOSTON (AP) -- A Harvard University professor who won the Nobel chemistry
prize in 1976 for work on chemical bonding has died. William Nunn Lipscomb
Jr. was 91.

His son, James Lipscomb, said Friday that Lipscomb died Thursday night at a
Cambridge, Mass., hospital of pneumonia and complications from a fall.

Several of his students also have won Nobels. Yale University professor
Thomas Steitz, who shared the 2009 chemistry prize, says Lipscomb was an
inspiring teacher who encouraged creative thinking.

The Ohio native grew up in Lexington, Ky., and students affectionately
referred to him as Colonel in reference to his upbringing. He graduated
from the University of Kentucky and got a doctorate at the California
Institute of Technology under Nobel laureate Linus Pauling.

Lipscomb is survived by his wife and three children.

[ccp4bb] oxford cryosystems series 600 control box

[Peter Moody]

The venerable 600 series cryostream I use on our Raxis is getting too
flakey, and as they are no longer supported I cannot get it fixed. Should
anyone be thinking of sending one to the skip, I should be very pleased to
hear from you (directy).

Peter Moody
University of Leicester
Leicester UK