[ccp4bb] PhD studentship ILL (France) / Keele University (UK)

[Daouda Traore]

Hi,

An exciting opportunity exists for a PhD student based in the Life Sciences
Group (https://www.ill.eu/lsg) at the Institut Laue-Langevin (ILL) in
France. The project will focus on structural characterisation of a DNA
transfer machinery and is of particular relevance to antibiotic resistance.
The methods used to study this system include neutron and X-ray diffraction
and cryo-EM, alongside the powerful range of technology platforms for
structural biology that are available at the Platform for Structural
Biology (PSB - see https://www.psb-grenoble.eu/). The Grenoble science
campus hosts the ILL neutron beam source, the ESRF synchrotron X-ray
source, and is very well equipped for advanced cryo-EM, including a newly
acquired Titan Krios microsciope.

The student will be based 100% in Grenoble and registered at Keele
University in the UK.

For further information, see

https://www.findaphd.com/phds/project/molecular-architecture-of-a-dna-transfer-machinery-and-its-contribution-to-the-dissemination-of-antibiotic-resistance/?p121089

https://www.ill.eu/careers/all-our-vacancies/phd-recruitment/open-phd-positions/

Regards

Daouda

[image: Logo ILL] 
Daouda A.K. TRAORE
Faculty of Natural Sciences
*Keele University*
Staffordshire ST5 5BG, United Kingdom
*&*
Life Sciences Group
*Institut Max von Laue - Paul Langevin (ILL)*
71, avenue des Martyrs - CS 20156
38042 Grenoble cedex 9 - France
+33 (0)4 76 20 94 94
d.tra...@keele.ac.uk or trao...@ill.eu



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[ccp4bb] Map grid passing from ccp4 refmac mask?

[Bernhard Rupp]

Dear Developers,

 

I am wondering if there is a way to entice the REFMAC ccp4i input mask to
accept and hand-off grid parameters into the subsequently

running FFTBIG if I select the 'Generate weighted difference maps' option?

 

Just a convenience issue. I can script it. 

 

Also the map file name despite selection (xyz.ccp4) gets changed to xyz.map
in the actual output.

 

Best, BR

 

--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

  http://www.hofkristallamt.org/

  b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




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[ccp4bb] Strange Pseudosymmetry Effects

[Jessica Bruhn]

Hello,

I am wondering if pseudosymmetry can cause weak reflections that mimic the
doubling of one unit cell axis' length. Has anyone seen something like this
before?

 I am processing data from a small molecule sample collected with electron
diffraction from multiple crystals. For the b axis, it is not clear if the
length should be 10A or 20A. There are spots with the correct spacing for
b=20A, but every other spot seems weaker than the spots along k if I choose
b=10A (this extends beyond (0,k,0)). I am unable to phase the b=20 data. I
have solved this structure in P1 with b=10 and found four molecules in the
ASU and in P212121 with b=10 resulting in one molecule in the ASU. In P1,
three of the four molecules adopt the same conformation, but the fourth
molecule is in an alternate conformation that causes only ~1/2 of the
molecule to be consistent with the first three. In P212121 I see density
for part of this alternative conformation, but the full molecule in this
alternate conformation cannot pack properly in P212121. Based on these
results and some orthogonal data, I think I should refine the solution in
P1 with b=10. Does it seem reasonable that pseudosymmetry is causing these
weak reflections along k hinting at a doubling of the b axis?

Thanks in advance!

Best,
Jessica

-- 
Jessica Bruhn, Ph.D
Principal Scientist
NanoImaging Services, Inc.
4940 Carroll Canyon Road, Suite 115
San Diego, CA 92121
Phone #: (888) 675-8261
www.nanoimagingservices.com



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Re: [ccp4bb] Strange Pseudosymmetry Effects

[Petrus Zwart]

Hi Jessica,

If you see spots and they fit a lattice, you should use them.  Use the b=10
solution in P1 that you have with 3 models (or two if one is iffy) and use
that as a start model for MR in b=20 and start searching for the rest.
Alternatively, use the b=10 model with stuff that looks decent and generate
a model for b=20 by adding in the lattice translations. This can be tricky,
especially when you are not in P1, so perhaps try the first option first.

Pseudo translational symmetry will do this to you btw:
https://journals.iucr.org/d/issues/2008/01/00/ba5111/ba5111.pdf , section
3.4.2

Regards
Peter


On Wed, May 27, 2020 at 7:00 PM Jessica Bruhn <
450e5de75376-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello,
>
> I am wondering if pseudosymmetry can cause weak reflections that mimic the
> doubling of one unit cell axis' length. Has anyone seen something like this
> before?
>
>  I am processing data from a small molecule sample collected with electron
> diffraction from multiple crystals. For the b axis, it is not clear if the
> length should be 10A or 20A. There are spots with the correct spacing for
> b=20A, but every other spot seems weaker than the spots along k if I choose
> b=10A (this extends beyond (0,k,0)). I am unable to phase the b=20 data. I
> have solved this structure in P1 with b=10 and found four molecules in the
> ASU and in P212121 with b=10 resulting in one molecule in the ASU. In P1,
> three of the four molecules adopt the same conformation, but the fourth
> molecule is in an alternate conformation that causes only ~1/2 of the
> molecule to be consistent with the first three. In P212121 I see density
> for part of this alternative conformation, but the full molecule in this
> alternate conformation cannot pack properly in P212121. Based on these
> results and some orthogonal data, I think I should refine the solution in
> P1 with b=10. Does it seem reasonable that pseudosymmetry is causing these
> weak reflections along k hinting at a doubling of the b axis?
>
> Thanks in advance!
>
> Best,
> Jessica
>
> --
> Jessica Bruhn, Ph.D
> Principal Scientist
> NanoImaging Services, Inc.
> 4940 Carroll Canyon Road, Suite 115
> San Diego, CA 92121
> Phone #: (888) 675-8261
> www.nanoimagingservices.com
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>


-- 

P.H. Zwart
Staff Scientist
Molecular Biophysics and Integrated Bioimaging &
Center for Advanced Mathematics for Energy Research Applications
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246

PHENIX:   http://www.phenix-online.org
CAMERA: http://camera.lbl.gov/
-



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Re: [ccp4bb] Strange Pseudosymmetry Effects

[Ethan A Merritt]

On Wednesday, 27 May 2020 18:49:23 PDT Jessica Bruhn wrote:
> Hello,
> 
> I am wondering if pseudosymmetry can cause weak reflections that mimic the
> doubling of one unit cell axis' length. Has anyone seen something like this
> before?

Yes.

>  I am processing data from a small molecule sample collected with electron
> diffraction from multiple crystals. For the b axis, it is not clear if the
> length should be 10A or 20A. There are spots with the correct spacing for
> b=20A, but every other spot seems weaker than the spots along k if I choose
> b=10A (this extends beyond (0,k,0)). I am unable to phase the b=20 data. I
> have solved this structure in P1 with b=10 and found four molecules in the
> ASU and in P212121 with b=10 resulting in one molecule in the ASU. 

> In P1, three of the four molecules adopt the same conformation, but the fourth
> molecule is in an alternate conformation that causes only ~1/2 of the
> molecule to be consistent with the first three. In P212121 I see density
> for part of this alternative conformation, but the full molecule in this
> alternate conformation cannot pack properly in P212121. Based on these
> results and some orthogonal data, I think I should refine the solution in
> P1 with b=10. Does it seem reasonable that pseudosymmetry is causing these
> weak reflections along k hinting at a doubling of the b axis?

This description makes me think also of a supercell.  This can happen
when, say, the position of one copy N is not compatible with all (N-1) of
the others positions.  Some unit cells contain (N-1) copies but not the
problematic N; other cells contain the N copy but miss one or more of
the others to make room.  This gives you a stochastic mix of cell
contents.  If it were truly random you'd see spots for a small cell
but the contents would have to be described by partially occupied sites.
But if there is a bias towards alternation of cells +N -N +N -N you
get a pseudo-doubling of that cell edge, matching your description.

Suggested reading:
Lovelace J, Petrícek V, Murshudov G, Borgstahl GEO.
Supercell refinement: a cautionary tale. Acta Crystallogr D Struct Biol. 2019 
Sep 1;75(Pt 9):852-860. 
doi: 10.1107/S2059798319011082. Epub 2019 Aug 28. PMID: 31478908; PMCID: 
PMC6719663.

I've had to deal with these in macromolecular crystals.
I would imagine that the same can happen for electron diffraction
but I can't point to any prior examples in the literature.

good luck!

Ethan

> Thanks in advance!
> 
> Best,
> Jessica
> 
> 


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



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Re: [ccp4bb] Map grid passing from ccp4 refmac mask?

[Eleanor Dodson]

In cco4i you can select “run and view com file” then edit the appropriate
command into the com file. Not sure if you can change the file name
extension on the command line though - I seem to remember extensions were
cast in stone to simplify. Cataloging outputs. But you can always rename
any file in the script? Eleanor

On Thu, 28 May 2020 at 02:31, Bernhard Rupp 
wrote:

> Dear Developers,
>
>
>
> I am wondering if there is a way to entice the REFMAC ccp4i input mask to
> accept and hand-off grid parameters into the subsequently
>
> running FFTBIG if I select the ‘Generate weighted difference maps’ option?
>
>
>
> Just a convenience issue. I can script it.
>
>
>
> Also the map file name despite selection (xyz.ccp4) gets changed to
> xyz.map in the actual output.
>
>
>
> Best, BR
>
>
>
> --
>
> Bernhard Rupp
>
> Crystallographiae Vindicis Militum Ordo
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429
>
> +43 676 571 0536
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
>
> --
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] Strange Pseudosymmetry Effects

[Eleanor Dodson]

Yes - in P1 if you have two molecules approximately related by
X y z. And x+ 1/2 y z say then the spots along the axis a* will have h=2n
weak.  And the sections with h even will have very weak spots. If you
calculate a Patterson for the data there will be a strong peak st 1/2, 0,0.
  But you say you can find a reasonable solution in p21 21 21? Have you
tried symmetry p21 with the 2fd axis along a* or c*?   Also it is possible
if you have multiple crystals the merging has combined crystals with
similar symmetry - is your 2 fold axes- but not exact. Look at the data
analysis to see if some crystals agree better than others.

On Thu, 28 May 2020 at 03:49, Ethan A Merritt  wrote:

> On Wednesday, 27 May 2020 18:49:23 PDT Jessica Bruhn wrote:
> > Hello,
> >
> > I am wondering if pseudosymmetry can cause weak reflections that mimic
> the
> > doubling of one unit cell axis' length. Has anyone seen something like
> this
> > before?
>
> Yes.
>
> >  I am processing data from a small molecule sample collected with
> electron
> > diffraction from multiple crystals. For the b axis, it is not clear if
> the
> > length should be 10A or 20A. There are spots with the correct spacing for
> > b=20A, but every other spot seems weaker than the spots along k if I
> choose
> > b=10A (this extends beyond (0,k,0)). I am unable to phase the b=20 data.
> I
> > have solved this structure in P1 with b=10 and found four molecules in
> the
> > ASU and in P212121 with b=10 resulting in one molecule in the ASU.
>
> > In P1, three of the four molecules adopt the same conformation, but the
> fourth
> > molecule is in an alternate conformation that causes only ~1/2 of the
> > molecule to be consistent with the first three. In P212121 I see density
> > for part of this alternative conformation, but the full molecule in this
> > alternate conformation cannot pack properly in P212121. Based on these
> > results and some orthogonal data, I think I should refine the solution in
> > P1 with b=10. Does it seem reasonable that pseudosymmetry is causing
> these
> > weak reflections along k hinting at a doubling of the b axis?
>
> This description makes me think also of a supercell.  This can happen
> when, say, the position of one copy N is not compatible with all (N-1) of
> the others positions.  Some unit cells contain (N-1) copies but not the
> problematic N; other cells contain the N copy but miss one or more of
> the others to make room.  This gives you a stochastic mix of cell
> contents.  If it were truly random you'd see spots for a small cell
> but the contents would have to be described by partially occupied sites.
> But if there is a bias towards alternation of cells +N -N +N -N you
> get a pseudo-doubling of that cell edge, matching your description.
>
> Suggested reading:
> Lovelace J, Petrícek V, Murshudov G, Borgstahl GEO.
> Supercell refinement: a cautionary tale. Acta Crystallogr D Struct Biol.
> 2019 Sep 1;75(Pt 9):852-860.
> doi: 10.1107/S2059798319011082. Epub 2019 Aug 28. PMID: 31478908; PMCID:
> PMC6719663.
>
> I've had to deal with these in macromolecular crystals.
> I would imagine that the same can happen for electron diffraction
> but I can't point to any prior examples in the literature.
>
> good luck!
>
> Ethan
>
> > Thanks in advance!
> >
> > Best,
> > Jessica
> >
> >
>
>
> --
> Ethan A Merritt
> Biomolecular Structure Center,  K-428 Health Sciences Bldg
> MS 357742,   University of Washington, Seattle 98195-7742
>
> 
>
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>
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>



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

[lyguo]

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



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