[ccp4bb] XSCALE bugfix

[Kay Diederichs]

Dear academic XDS/XSCALE users,

there's a bug in XSCALE, in the BUILT=20190606 of the XDS program package. The 
bug was not in present in earlier versions. It is corrected in the latest 
BUILT=20190806 which is available from the download section of 
http://xds.mpimf-heidelberg.mpg.de . 

The release notes in the documentation that can be downloaded as a tar-file 
from that site is updated. The release notes at 
http://xds.mpimf-heidelberg.mpg.de/html_doc/Release_Notes.html will soon be 
updated.

Those XSCALE users who downloaded BUILT=20190606 should upgrade, and consider 
re-xscaling. 
best wishes,

Kay



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Re: [ccp4bb] How to include in refinement high resolution shells with VERY low completeness ?

[Ivan Shabalin]

Pavel,

Sorry for an unclear sentence. What I meant was:

My conclusion is that  "no fill-in" option might be tried at some stages 
for datasets with low high res completeness. But, if a dataset ALSO has 
low completeness in low-medium shells, then extra caution should be 
applied. In my case, 2fofc maps looked really weird, likely due to low 
res completeness and "no fill-in".


Thanks for sharing great example!

Ivan



On 8/7/19 17:18, Pavel Afonine wrote:

Hi Ivan,

My conclusion is that  "no fill-in" option might be tried at some
stages, but with caution, especially for datasets with poor low res
completeness.


I'm guessing you really meant *high*, not low. More or less repeating 
what others said already.. Correcting for low res completeness doesn't 
add high-res details and so has lesser risk of introducing model bias at 
atomic level. Contrary, filling in high-res terms is likely to 
noticeably bias the map at atomic level of detail.


Here is one of my favorite examples of what missing low-res data can do 
to your map:

http://cci.lbl.gov/~afonine/tmp/1nh2.pdf

Pavel







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Re: [ccp4bb] How to include in refinement high resolution shells with VERY low completeness ?

[Pavel Afonine]

Hi Ivan,


> My conclusion is that  "no fill-in" option might be tried at some
> stages, but with caution, especially for datasets with poor low res
> completeness.
>

I'm guessing you really meant *high*, not low. More or less repeating what
others said already.. Correcting for low res completeness doesn't add
high-res details and so has lesser risk of introducing model bias at atomic
level. Contrary, filling in high-res terms is likely to noticeably bias the
map at atomic level of detail.

Here is one of my favorite examples of what missing low-res data can do to
your map:
http://cci.lbl.gov/~afonine/tmp/1nh2.pdf

Pavel



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Re: [ccp4bb] How to include in refinement high resolution shells with VERY low completeness ?

[Ivan Shabalin]

Dear Eleanor and Kay,

Thanks for pointing out that the difference maps does not show model 
bias due to "fill-in".


The difference maps generated with "fill-in" and without (mapcalculate 
free include) look somewhat different for another dataset I tried. But, 
these differences are small.


Notably, 2fofc map caluculated with "mapcalculate free include" look 
weird for this dataset. This outcome is somewhat expected due to low 
completeness in lower shells (yes, this dataset is problematic). In the 
first dataset, which has good low res completeness, omit maps looked 
somewhat better, as I  wrote before.


My conclusion is that  "no fill-in" option might be tried at some 
stages, but with caution, especially for datasets with poor low res 
completeness.


Many thanks to everyone!

Ivan

With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA 22908
https://www.linkedin.com/in/shabalinig/
https://minorlab.org/person/ivan_s/

On 8/6/19 09:39, Eleanor Dodson wrote:
There are certainly some problems with REFMAC after an anisotropy 
correction. The FreeR flags and D corrections are organised in spherical 
shells, whereas the D aniso volume is elliptical..



As Kay points out the REFMAC map coefficient for a difference map is 0 
if there is no measurement so there is no bias in those maps.


the 2mFo-DFc maps do set the map coefficient to D Fc if there is no 
measurement, potentially introducing bias.


The thinking is that when a large low resolution term is missing it is 
better to approximate it to something realistic, rather than set it to 0.
For high weak resolution data D Fc will also probably be insignificant 
and there would be very little gain by including it, and the possibility 
of introducingbias..


However nowadays the data collection techniques usually provide pretty 
complete data at low resolution,


On Tue, 6 Aug 2019 at 07:44, Kay Diederichs 
mailto:kay.diederi...@uni-konstanz.de>> 
wrote:


Dear Ivan,

one thing I forgot to mention: I think the difference maps should
not show model bias due to "fill-in". This is because the term
D*Fcalc that is filled in as a replacement for m*Fobs is just
compensated by the term D*Fc that is subtracted when forming the
m*Fobs - D*Fcalc difference coefficients.
This means that when building the model, you can let yourself be
guided primarily by the difference maps. These will not suffer from
model bias due to fill-in.

I like the idea of the "shaping the MTZ file" that Robbie suggests,
but I still need to work out the proper sftools commands, like those
at http://staraniso.globalphasing.org/test_set_flags_about.html .

best,
Kay

On Mon, 5 Aug 2019 17:44:56 -0400, Ivan Shabalin
mailto:iva...@iwonka.med.virginia.edu>> wrote:

 >Dear Kay,
 >
 >Thanks a lot for your answers!
 >
 >To my best understanding, REFMAC does not have an option of for
 >restoring reflections only in certain resolution shells. But, it
should
 >not be a problem for datasets with good completeness in low
resolution
 >shells. Also, refinement against intensities is available only for
twin
 >refinement.
 >
 >I will take this as a conclusion for datasets with good low
resolution
 >completeness: "even if the visual effect of weak reflections on
the map
 >may be low, the errors in the model coordinates will be less if
the weak
 >amplitudes are used in refinement"
 >
 >Thanks!
 >
 >Ivan
 >
 >
 >With best regards,
 >Ivan Shabalin, Ph.D.
 >Research Scientist,
 >Department of Molecular Physiology and Biological Physics,
 >University of Virginia,
 >1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
 >Charlottesville, VA 22908
 >https://www.linkedin.com/in/shabalinig/
 >https://minorlab.org/person/ivan_s/
 >
 >On 8/3/19 04:32, Kay Diederichs wrote:
 >> Dear Ivan,
 >>
 >> On Thu, 1 Aug 2019 22:10:36 -0400, Ivan Shabalin
mailto:iva...@iwonka.med.virginia.edu>> wrote:
 >>
 >>> Dear CCP4BB,
 >>>
 >>> There seems to be a general consensus for extending data to higher
 >>> resolution to include as much meaningful data as possible.
"Meaningful"
 >>> can be defined in different ways. I heard/read opinions such as 0.5
 >>> CC1/2, 0.3 CC1/2, 0.15 CC1/2,
 >>
 >> This is numerology - why not 0.3 or 0.12345?  The EM
community has agreed on the "gold standard" of 0.143 for FSC which
has a similar definition as CC1/2 - this value is chosen because the
quantity analogous to CC* is then 0.5 !
 >>
 >>> and stepped (paired) refinement. The
 >>> latter seems to be one of the most rigorous options according
to many
 >>> crystallographers.
 >>>
 >>> Including 

[ccp4bb] Stanford-SLAC Cryo-EM Center (S2C2) Workshop for Beginners - Sep. 11-13, 2019

[Dunn, Lisa B.]

S2C2 Workshop - Cryo-EM for Beginners September 11-13, 2019


Location: SLAC National Accelerator Laboratory, Menlo Park, CA USA


Stanford-SLAC Cryo-EM Center (S2C2) is offering a training workshop on 
experimental aspects of cryo-EM tailored to beginners.  This workshop will be 
held at SLAC National Accelerator Laboratory between September 11 and 13, 2019. 
Preference of trainees is given to individuals who have research projects ready 
for cryo-EM investigations and have a background in structural biology. This 
workshop will consist of three days of morning lectures and afternoon hands-on 
training sessions.  Onsite attendance for the lecture sessions is limited to 
~40 participants with additional access provided via Zoom teleconferencing.  
The hands-on sessions are limited to 8 participants. If you are interested, you 
may apply before August 31, 2019.


There is no fee for this workshop.  The workshop agenda and application form 
can be found at: https://cryoem.slac.stanford.edu/s2c2/training/workshops


We look forward to providing this training in September!



The Organizers (Wah Chiu, Georgios Skiniotis, Britt Hedman, Michael Schmid)


The S2C2 is supported by the National Institutes of Health Common Fund 
Transformative High Resolution Cryo-Electron 
Microscopy program.



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[ccp4bb] Postdoctoral Fellow Position at UT Southwestern Medical Center on ‘Chromatin Structure and Epigenetics’

[Xin Liu]

Dear Colleagues,


A Postdoctoral Fellow position is available for a highly motivated researcher 
in Dr. Xin Liu’s group at UT Southwestern Medical Center.  The Liu Lab is also 
a core member of Cecil H. and Ida Green Center for Reproductive Biology 
Sciences.  The overarching goal of the Liu Lab is to understand the cellular 
regulation of dynamic chromatin structure, which is well known to impact both 
normal and disease development.  The Liu Lab is particularly interested in 
elucidating structure and function of large macromolecular assemblies that 
mediate formation of heritable high-order chromatin structure.  A current focus 
includes Polycomb Repressive Complexes, which modify histones, alter chromatin 
structure, and maintain cell identity during development.  To achieve the 
research goal, we leverage a combination of advanced research tools, including 
biochemical reconstitution (e.g. protein-protein, protein-nucleosome, and 
protein-non-coding RNA complexes), X-ray crystallography, cryo-EM, proteomics, 
and genomics by next-generation sequencing.  The study of structure-function 
relationships in the Liu Lab is typically carried out in a variety of cancer 
and pluripotent stem cells.  Additional information is available here: 
http://profiles.utsouthwestern.edu/profile/127166/xin-liu.html



Applicants with background or interest in structural biology, protein and 
nucleic acid biochemistry, and chromatin biology are encouraged to apply.  
Trainees will have opportunities to learn the existing research tools in the 
lab as outlined above and will be encouraged to develop new cutting-edge tools 
as the project evolves.  Candidates must hold a Ph.D. and/or M.D. degree with 
first author publications and should submit a CV and contact information of 3 
references to the PI by e-mail at: 
xin@utsouthwestern.edu



UT Southwestern Medical Center is an Affirmative Action/Equal Opportunity 
Employer.  Women, minorities, veterans and individuals with disabilities are 
encouraged to apply.  UT Southwestern Medical Center offers extraordinary 
benefits for employees (more information is available here: 
https://jobs.utsouthwestern.edu/benefits.html).


Sincerely,


Xin Liu

---
Xin Liu, Ph.D.

Associate Professor
W.W. Caruth, Jr. Scholar in Biomedical Research
Cecil H. and Ida Green Center for Reproductive Biology Sciences ?
UT Southwestern Medical Center

5323 Harry Hines Blvd., J7.104A
Dallas, TX 75390-8511
Phone: 214-648-2493
Fax: 214-648-0383
E-mail: xin@utsouthwestern.edu





UT Southwestern


Medical Center



The future of medicine, today.




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[ccp4bb] Lectureship Positions University of Kent

[Gary Thompson]

We have two Jobs advertised at the University of Kent that may be of interest 
to structural biologists with expertise in macro molecular crystallography.

https://jobs.kent.ac.uk/Vacancy.aspx?ref=STM-032-19

The School of Biosciences has a long and continuing interest in structural 
biology with several groups exploiting NMR and Macromolecular Crystallography 
to study a wide range of problems. These include infection and drug resistance, 
cancer and age-related diseases, cellular architecture and dynamics and 
reproduction, evolution and genomics and industrial biotechnology.  The School 
of Biosciences consistently has time as a BAG at Diamond and has recently 
invested in a new Mosquito LCP System with humidity control for crystallisation 
drop set up. Other facilities available for structural biologists include a 
well equipped Biomolecular Science Facility  (electrospray and MALDI-TOF mass 
spectrometers, peptide synthesisers, CD etc) an in  house X-Ray source in the 
School of Physical Sciences (Rigaku Oxford Diffraction Supernova)  and a 
dedicated Biological NMR Facility with BAG access at the UK national NMR 
facilities at the Crick and Birmingham. Applications close 23.59 hours BST 19th 
August. See Job Description for further details.

regards
gary

---
Dr Gary S Thompson

School of Biosciences, University of Kent,
Canterbury,  Kent,  England,  CT2 7NZ


tel: 01227 82 7117
e-mail: g.s.thomp...@kent.ac.uk
orchid: orcid.org/-0001-9399-7636
---




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[ccp4bb] TIME TO REGISTER: 33rd Rhine Knee Meeting Structural Biology - October 2019 - Lausanne (Switzerland)

[Pojer Florence]

Dear Colleagues,

The 33rd Rhine Knee meeting on Structural Biology (Regio 2019) will take place 
on the shore of Lac Leman in  October 2019; Monday 14th (after 5pm) to 
Wednesday 16th (until 2pm) October.

One of the very positive aspect of this meeting is to allow young researchers 
to present their work in front of their peers. So do not hesitate to come and 
present your latest discoveries!
The meeting is also limited to 90 participants, creating an amazing environment 
for collaborations and sharing  knowledge on the latest techniques in the 
Structural Biology field.

Big Thanks to the keynote speakers:
 Dr. Hugues Nury (IBS, 
Grenoble),
 Specialist in structural biology of membrane machineries
 Dr. Martin Pilhofer (ETHZ, Zurich), Expert in 
electron cryo-tomography with a special focus on in situ bacterial 
macromolecular complexes.
 Dr. Gaia Barazzetti (UNIL, 
Lausanne),
 Researcher in scientific integrity & misconducts. Her talk will be followed by 
an open discussion.

TOPICS include:

  *   Integrative Structural Biology
  *   Biophysical Techniques
  *   X-ray Crystallography
  *   Bio-NMR
  *   Cryo EM
  *   Drug Discovery
  *   Methods Developments
  *   Synchrotrons news
  *   Scientific Integrity

REGISTRATION HERE

Additional info and preliminary agenda: 
https://www.epfl.ch/research/facilities/ptpsp/home-ppscf/news/
The venue is at Hotel du Leman:  https://hotel-leman.ch/en/
An excursion will take place on the Tuesday afternoon  at Chaplin’s 
world, located at walking distance from the 
venue.

Looking forward to seeing you in October!

Best, Florence Pojer


 
---
Florence Pojer, PhD
Head of the Protein Production and Structure Core Facility – PTPSP
EPFL, Lausanne, Switzerland
Phone: +41216931976
https://www.epfl.ch/research/facilities/ptpsp





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