Re: [ccp4bb] Strange Pseudosymmetry Effects

2020-05-27 Thread 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] Strange Pseudosymmetry Effects

2020-05-27 Thread 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:
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>


-- 

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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[ccp4bb] Strange Pseudosymmetry Effects

2020-05-27 Thread 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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[ccp4bb] Map grid passing from ccp4 refmac mask?

2020-05-27 Thread 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] PhD studentship ILL (France) / Keele University (UK)

2020-05-27 Thread 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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