[ccp4bb] Postdoctoral Position available - University of Warsaw, Poland

[Paulina Dominiak]

Dear colleagues,

I would like to draw your attention to a post-doctoral position 
available in my research group.

For all the details, please see the complete call text below.
If you need any further information, please contact me directly.

Best regards,
Paulina Dominiak


An announcement for Post-doctoral position

Position of Post-doctoral Researcher in the OPUS project entitled

"More accurate models of the electrostatic potential of biological 
macromolecules and organic crystals necessary for proper interpretation 
of data from cryo-electron microscopy and from electron diffraction – 
feasibility study"


financed by NCN is open for application.

Project leader: dr hab. Paulina M. Dominiak, prof. UW

Available positions: 1

Project description:
The Dominiak’s group works on developing new methods of electron density 
modelling for X-ray and electron crystallography, chemistry and 
structural biology. The project aims at development of new models of 
electrostatic potentials for electron crystallography. The models will 
considerably deviate from the conventional spherical independent atom 
model currently used. With new models more  information should be 
extracted from electron scattering experiments on biological 
macromolecules and organic crystals, and improved quality of geometric 
data and quantitative estimates of molecular electrostatic potentials 
should become easily available. For further information see 
http://cnbch.uw.edu.pl and http://www.chem.uw.edu.pl.


Position description:
You will be mainly responsible for development and verification of new 
databanks of atomic electron densities on the basis of existing procures 
published in: Acta Cryst. 2012, A68, 139; JCTC, 2014, 10, 1652; 
ChemPhysChem, 2016, 17, 2455; Acta Cryst. 2017, B73, 610.


We are looking for motivated candidates with:

-a PhD degree in chemistry or related fields at the moment of starting 
the job (PhD defended not later than 7 years ago according to NCN 
regulations, see www.ncn.gov.pl)
-experience in crystallography OR/AND computational chemistry proven by 
scientific article publications
-knowledge of macromolecular crystallography OR/AND proven experience in 
high-resolution x-ray diffraction charge density measurements
-basic programing skills OR/AND practical experience in script 
usage/writing and proven ability to work with large amount of data
-experience with structure refinement against electron diffraction or 
single particle cryoEM data will be an advantage

-well-developed analytical skills
-good knowledge of written and spoken English
-written and spoken presentation skills
-ability to work as part of a team
We offer:
a temporary employment contract with the University of Warsaw:
-full time position
-a salary approx. 5000 PLN per month (net salary, after taxes and other 
deductions)

-for one year with a possible extension upto three years
-appointment starting in November 2018 (the competition may be repeated 
until a suitable candidate who fulfils all requirements is found)


Required documents (in English):
-Curriculum Vitae (including list of scientific articles, conference 
presentations, awards, international internships,  scholarships, 
workshops, participation in research projects),
-a motivation letter (What are your scientific interests? What are your 
key strengths and achievements? Why do you want to work in the project?),

-information on the processing of personal data (see the text below),
-two recommendation letters (at least one from direct supervisor) sent 
by the referees directly  to prof. Dominiak (pdo...@chem.uw.edu.pl).


Please submit the documents no later than 26 October 2018 to: 
pdo...@chem.uw.edu.pl (PDF is the preferred format). E-mail entitled: 
“Post-Doc position”


Selected candidates may be invited by e-mail, no later than  30 October 
2018, to participate in interview.  The interview will take place on 5 
or 6 November 2018 in person or via Skype or phone. The results of the 
competition will be delivered to selected candidates by e-mail till 15 
November 2018. In the case of not signing the contract by the candidate, 
due to the resignation, we reserve the right to choose the next 
candidate from the ranking list.


 
INFORMATION ON THE PROCESSING OF PERSONAL DATA
INFORMATION CLAUSE
Pursuant to Article 13 of Regulation (EU) 2016/679 of the European 
Parliament and of the Council of 27 April 2016 on the protection of 
natural persons with regard to the processing of personal data and on 
the free movement of such data, and repealing Directive 95/46/EC 
(General Data Protection Regulation), University of Warsaw hereby informs:
1.	The Controller of your personal data is the University of Warsaw with 
its registered office at Krakowskie Przedmieście 26/28, 00-927 Warszawa;
2.	The Controller has designated the Data Protection Officer who 
supervises the processing of personal data, and who can be contacted via 
the following e-mail address: i...@adm.uw

Re: [ccp4bb] Rietveld refinement of polycrystalline electron diffraction data

[Paulina Dominiak]

Dear Kamil and Dimitris,

I wonder what kind of scattering factors are mentioned below programs 
using for Rietfveld refinement? Are these from IT for electron scattering?


Best,

Paulina


W dniu 12.11.2020 o 07:35, Dimitris Triandafillidis pisze:

Dear Kamil,

Since you have an initial model that is presumably close to what you 
expect to find in your sample, then Rietveld refinement is the right 
choice. In cases where no initial model is available, other types of 
refinement are suitable, such as Pawley or Le Bail, which refine 
lattice and peak shape parameters only.


Regarding the order in which parameters are introduced to a fit, a 
good starting point would be:

- lattice parameters and zero shift
- peak shape parameters and scale factor
- background terms
- atomic positions
Depending on the quality of your data and the nature of your sample, 
more parameters could be refined (i.e. atomic displacement parameters, 
preferred orientation, absorption etc.).


My suggestion would be to get a better understanding of the effect of 
each parameter to the fit, in order to troubleshoot your refinement 
more effectively. For example, peak positions depend on lattice 
parameters (and space group setting), therefore refining e.g. the 
scale factor would not help much if expected peak positions are in the 
wrong place. The following article might be helpful to you.
McCusker, L.B., Von Dreele, R.B., Cox, D.E., Louër, D., Scardi, P., 
1999. Rietveld refinement guidelines. Journal of Applied 
Crystallography 32, 36–50. https://dx.doi.org/10.1107/S0021889898009856


As for the single peak not being explained by the fit, it could be due 
to deviations in lattice parameters, but in that case more than one 
peak would not match. If every other peak fits nicely and only one 
does not, I would think that it is due to coexistance of a second, 
trace, crystalline phase in the sample. In most refinement software 
you have the option of excluding a peak from refinement. Refining 
atomic positions would not help, as these change the relative peak 
intensities, not peak positions. However, if you could share a few 
images of the fit, it would really help to better understand what's 
going on.


Finally, with regards to software, you could also try GSAS 
. It is one of the 
most widely used software for powder diffraction and it is free. There 
is also a mailing list 
, consisting 
mainly of powder diffractionists, and a handful collection of 
tutorials 
.


Best wishes,
Dimitris


On Thu, Nov 12, 2020 at 12:18 AM Kamil Krawczyk 
mailto:kamil.krawczyk7...@gmail.com>> 
wrote:


Hello!

First, apologies if the scope of the question is beyond that of
the listserv - I was recommended this discussion page through a
colleague.

I am incredibly new to refinement, and have been trying to employ
the use of Rietveld refinement to better determine the crystal
structure of my lead sulfide (PbS) quantum dots. Data was acquired
as images on a home-built tabletop time-resolved electron
diffraction setup, and converted to diffractogram through a
combination of center finding and background subtraction. However,
since these are small (~ 5 nm), and we are certainly sampling the
ensemble average (as our focused beam is about 120 um in
diameter), our pattern is that of a polycrystalline sample.

>From what I've encountered in my research, Rietveld is best
suited for this case. I have taken an initial structure as
inferred from literature/the bulk and refined that (relatively
successfully to a Rwp value of ~2 - 6%). I do have a few questions
regarding this process as I believe I am not being as rigorous as
possible:

- is there a 'best practices' order of refinement operations? e.g.
refine the lattice parameters first, then peak profiles, etc.
- there is a single peak that is not matching (likely due to a
slight deviation in atomic positions from the expected simple
cubic structure) - is refinement capable of moving individual
atoms or clusters of atoms to better match a small, unaccounted
for reflection?

For what it's worth, I have been using Reflex in Materials Studio;
if there is a more appropriate software for this application, I
would be happy to hear!

If any additional clarification is need, I'll fill it in!

Best,
Kamil



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