[ccp4bb] RapiData 2018 application reminder

[Smith, Clyde]

Hi all,


Just a reminder that the applications for the RapiData 2018 @ SSRL workshop 
close this coming Friday December 22. The workshop will be help from April 
22-27 2018 on the SLAC campus. Please visit the course website (below) and 
click on the Registration link to apply. We look forward to seeing you all out 
in sunny California in April 2018!


http://smb.slac.stanford.edu/news/rapidata/rapidata-2018/


Thanks and happy holidays,

Clyde Smith, Ana Gonzalez and Silvia Russi

(Organizers)

[ccp4bb] opening in Zbyszek Otwinowski lab

[Zbyszek Otwinowski]

Dear All,

I have an opening in my laboratory at UT Southwestern for someone who would like 
to work on multi-crystal data processing in X-ray crystallography and/or 
low-resolution model building both in X-ray crystallography and cryo-EM. The 
ideal candidate will have good programming skills (e.g. C, C++, Swift), 
excellent understanding of linear algebra, and previous experience with the 
experimental side of any data-intensive field. A knowledge of CUDA programming 
and data mining techniques is a plus.


Please send to z...@work.swmed.edu a 1-page resume containing: a link to your 
Google Scholar profile and other information about you that you consider to be 
the most important. Although the deadline for the application is February 15th, 
I will be interviewing candidates by Skype or in person (for Texas-based 
applicants) as soon as they are identified.


Zbyszek Otwinowski
UT Southwestern Medical Center  
5323 Harry Hines Blvd., Dallas, TX 75390-8816
(214) 645 6385 (phone) (214) 645 6353 (fax)
zbys...@work.swmed.edu

Re: [ccp4bb] New Ligand building and refining

[Paul Emsley]

On 19/12/2017 14:10, YUVARAJ I wrote:

Dear All,
how to built a new ligand and refine the pdb, since the refmac is failed with 
the following message
/Refmac died because it encountered a ligand not present in the monomer libraries it has read (i.e. the 
default CCP4 libraries plus any library you provided through the GUI). To continue, you have a number of 
options./

/
/
I would be very much grateful, if you could send me the protocol links to built and add a new ligand in the 
library.


One doesn't add a new ligand to the library. One uses a dictionary generator (as it seems that you know 
because you have added a ligand to your model) and the cif output of that is added as "LIB in" in the GUI. 
The model atoms and residue name must match those in the dictionary, needless to say.


Regards,

Paul.

Re: [ccp4bb] New Ligand building and refining

[Eleanor Dodson]

Do you have a smiles string for the ligand?
Acedrg will read that and create a dictionary for you.
Eleanr

On 19 December 2017 at 14:10, YUVARAJ I  wrote:

> Dear All,
> how to built a new ligand and refine the pdb, since the refmac is failed
> with the following message
> *Refmac died because it encountered a ligand not present in the monomer
> libraries it has read (i.e. the default CCP4 libraries plus any library you
> provided through the GUI). To continue, you have a number of options.*
>
> I would be very much grateful, if you could send me the protocol links to
> built and add a new ligand in the library.
>
> Thank you
> Regards
> Yuvaraj
>

[ccp4bb] Post-doctoral position in structural biology – I2BC (Orsay) and Institut Pasteur (Paris)

[Claudine Mayer]

A Postdoctoral position is available to work on a hot topic that links 
meiotic recombination and DNA topology control. The project, 
co-supervised by Profs Patrick Forterre and Claudine Mayer, aims to 
unveil the molecular mechanisms of double-strand breaks catalyzed by 
plant topoisomerase VI. The work will be performed in the team of 
Jacques Oberto at I2BC (Orsay, France) and the laboratory of Pedro 
Alzari at Institut Pasteur (Paris, France).


Various methods in structural biology(mainly X-ray crystallography but 
also cyo-EM), combined with enzymology and biophysics will be used to 
gain insights into the understanding of these fascinating nanomachines. 
The candidate will benefit from a large and rich scientific environment 
that extends to plant genetics as the project is part of an integrated 
program that includes collaboration with the team of Mathilde Grelon 
(INRA Versailles).


We seek a highly motivated candidate with a Ph.D. in the field of 
structural biology and with strong experience in protein biochemistry 
(production, purification and enzymatic assays). Experience in 
macromolecular crystallography is a plus, but not a requirement.


Remuneration: according to salary scale and experience.The position is 
open immediately and applications will be accepted until the position is 
filled.


Send cover letter, CV and two references by e-mail to ma...@pasteur.fr 
and patrick.forte...@pasteur.fr 




Selected publications related to the position:

Vrielynck N, Chambon A, Vezon D, Pereira L, Chelysheva L, De Muyt A, 
Mézard C, Mayer C, Grelon M. A DNA topoisomerase VI-like complex 
initiates meiotic recombination.


Science. 2016 Feb 26;351(6276):939-43. doi:10.1126/science.aad5196. 
PubMed PMID: 26917763.


Gadelle D, Krupovic M, Raymann K, Mayer C, Forterre P. DNA topoisomerase 
VIII: a novel subfamily of type IIB topoisomerases encoded by free or 
integrated plasmids in Archaea and Bacteria.


Nucleic Acids Res. 2014 Jul;42(13):8578-91. doi: 10.1093/nar/gku568. 
Epub 2014 Jul 2. PubMed PMID: 24990376.



Best wishes

--

[ccp4bb] New Ligand building and refining

[YUVARAJ I]

Dear All,
how to built a new ligand and refine the pdb, since the refmac is failed
with the following message
*Refmac died because it encountered a ligand not present in the monomer
libraries it has read (i.e. the default CCP4 libraries plus any library you
provided through the GUI). To continue, you have a number of options.*

I would be very much grateful, if you could send me the protocol links to
built and add a new ligand in the library.

Thank you
Regards
Yuvaraj

Re: [ccp4bb] Eiger 16M detector in HKL2000

[White, Mark]

Aidong,

I had a similar issue with the latest version of HKL2000. I had outsmarted 
myself by using symbolic links to the HKL executables. The HKL paths must be 
setup correctly for it to be able to find all the files necessary to read and 
decode the .h5 files.

Best regards
Mark

Sent from my iPhone

On Dec 19, 2017, at 2:23 AM, Aidong Han 
> wrote:

Probably it is the reason. We are working on upgrading our HKL and getting a 
new license. I will let you know when our problem is solved. Thank you so much. 
 Aidong

On Dec 19, 2017, at 2:49 PM, Raghurama P Hegde 
> wrote:

Dear Aidong,

As Dr. Förster has rightly pointed out you need to have the latest version of 
HKL2000 to work with the HDF5 files from the Eiger detectors and as you must be 
aware the HKL2000 license should include use of Eiger detectors. We have 
recently used HKL2000 to process data from MASSIF-3 beamline at ESRF which uses 
a EIGER X 4M detector but we had to upgrade to the latest version of HKL2000.

With regards,
Raghu


From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]On Behalf Of Andreas 
Förster
Sent: Tuesday, December 19, 2017 11:47
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Eiger 16M detector in HKL2000

Dear Aidong,

as I don't have access to HKL2000 myself, I can't tell you what might need to 
be done to have the software display EIGER X 16M images.  Wladek showed me that 
it was possible.  It might just be a question of getting the latest version.

There are alternatives to HKL-2000.

DIALS can process EIGER data with no questions asked 
(https://dials.github.io/).
  It is free, open-source software.  DIALS exists as a powerful command line 
tool but can also be run through the xia2 pipeline 
(https://xia2.github.io/).
  Both are part of CCP4, but I'd recommend installing the latest DIALS nightly 
because development is rapid.  The developers respond quickly to questions.

XDS can process EIGER data 
(http://xds.mpimf-heidelberg.mpg.de/html_doc/XDS.html).
  It is free to academic users.  To process data in HDF5 format (*.h5), make 
sure to download the neggia plugin 
(https://www.dectris.com/support/downloads/software/neggia,
 free, but registration required) and adjust the LIB= parameter to point to 
where the plugin is saved.  XDS is a command line tool, but several GUIs exist.

Please give DIALS or XDS a try and tell me how you get along.  If you continue 
to encounter problems, let me and the beamline staff at SSRF know.

All best.



Andreas



On Tue, Dec 19, 2017 at 6:48 AM, Aidong Han 
> wrote:
Hi All,

We have recently collected several data sets in the Shanghai synchrotron 
facility with a newly installed Eiger 16M. However, we are not able to process 
these data using our home HKL2000 package. Even though we can easily add this 
detector in, we can not display images. I believe ours has not been properly 
set up. While we are still waiting for a response from HKL2000 administration 
managers (it has been a few days), I wonder whether someone can provide me your 
solution since this detector has been in market for more than a year. Thank you 
for your help.

Sincerely,

Aidong

[ccp4bb] ReNaFoBiS. First Announcement Oleron 2018.

[VIE]

ReNaFoBiS. First Announcement Oleron 2018.

We are pleased to announce the 5th RéNaFoBiS Oléron workshop, dedicated to 
Integrative Structural Biology, that will take place on the Oléron island 
(France), from June the 1st until June the 8th, 2018. The main objective of 
this workshop is to offer a theoretical and practical training in the different 
techniques used in integrative structural biology (X-ray diffraction, small 
angle X-ray scattering, NMR, cryo-electron microscopy, sample preparation for 
structural biology,  biophysical methods to study and characterize 
macromolecular interactions). The goals are to explain and illustrate, to an 
audience mainly composed of doctoral students and young researchers, the 
contributions and limitations of each method with a strong emphasis on their 
complementarity and future developments.
The official language of the workshop is French but presentations may be given 
in English, depending on the overall profile of the students. For practicals, 
English and French speaking groups may be organised.

Registration is will open in January 2018 on the web site: 
https://ecolebios2018.sciencesconf.org/
Deadline for registration: April 9, 2018 (maximum number of participants: 25)
Applications will be evaluated upon deposition.
More information on the French Initiative ReNaFoBiS : http://www.renafobis.fr/

Best  regards
Jean Cavarelli
National ReNaFoBiS Coordinator

--

Jean Cavarelli
Professor of Structural Biology
Tél : +33 (0)3 69 48 52 74
jean.cavare...@unistra.fr
Structural Biology of Epigenetic Targets
Integrated Structural Biology Department
IGBMC. UMR7104 CNRS-UDS, INSERM U964.
F - 67404 Illkirch

Re: [ccp4bb] Eiger 16M detector in HKL2000

[Aidong Han]

Probably it is the reason. We are working on upgrading our HKL and getting a 
new license. I will let you know when our problem is solved. Thank you so much. 
 Aidong

On Dec 19, 2017, at 2:49 PM, Raghurama P Hegde  wrote:

> Dear Aidong,
>  
> As Dr. Förster has rightly pointed out you need to have the latest version of 
> HKL2000 to work with the HDF5 files from the Eiger detectors and as you must 
> be aware the HKL2000 license should include use of Eiger detectors. We have 
> recently used HKL2000 to process data from MASSIF-3 beamline at ESRF which 
> uses a EIGER X 4M detector but we had to upgrade to the latest version of 
> HKL2000.
>  
> With regards,
> Raghu
>  
>  
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]On Behalf Of Andreas 
> Förster
> Sent: Tuesday, December 19, 2017 11:47
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Eiger 16M detector in HKL2000
>  
> Dear Aidong,
>  
> as I don't have access to HKL2000 myself, I can't tell you what might need to 
> be done to have the software display EIGER X 16M images.  Wladek showed me 
> that it was possible.  It might just be a question of getting the latest 
> version.
>  
> There are alternatives to HKL-2000.
>  
> DIALS can process EIGER data with no questions asked 
> (https://dials.github.io/).  It is free, open-source software.  DIALS exists 
> as a powerful command line tool but can also be run through the xia2 pipeline 
> (https://xia2.github.io/).  Both are part of CCP4, but I'd recommend 
> installing the latest DIALS nightly because development is rapid.  The 
> developers respond quickly to questions.
>  
> XDS can process EIGER data 
> (http://xds.mpimf-heidelberg.mpg.de/html_doc/XDS.html).  It is free to 
> academic users.  To process data in HDF5 format (*.h5), make sure to download 
> the neggia plugin (https://www.dectris.com/support/downloads/software/neggia, 
> free, but registration required) and adjust the LIB= parameter to point to 
> where the plugin is saved.  XDS is a command line tool, but several GUIs 
> exist.
>  
> Please give DIALS or XDS a try and tell me how you get along.  If you 
> continue to encounter problems, let me and the beamline staff at SSRF know.
>  
> All best.
>  
>  
>  
> Andreas
>  
>  
>  
> On Tue, Dec 19, 2017 at 6:48 AM, Aidong Han  wrote:
> Hi All,
> 
> We have recently collected several data sets in the Shanghai synchrotron 
> facility with a newly installed Eiger 16M. However, we are not able to 
> process these data using our home HKL2000 package. Even though we can easily 
> add this detector in, we can not display images. I believe ours has not been 
> properly set up. While we are still waiting for a response from HKL2000 
> administration managers (it has been a few days), I wonder whether someone 
> can provide me your solution since this detector has been in market for more 
> than a year. Thank you for your help.
> 
> Sincerely,
> 
> Aidong