[ccp4bb] Macromolecular Crystallography workshop in South America

[Alejandro Buschiazzo]

Dear colleagues,

We are pleased to announce our sixth edition of the Workshop: 

Macromolecular Crystallography School "From data processing to structure 
refinement and beyond", to be held at the Institut Pasteur de Montevideo 
(Uruguay).

http://pasteur.uy/mx2017 

Dates: November 13 - 23, 2017

Confirmed speakers and tutors (so far... a few more may join the crew): 

Alejandro Buschiazzo, Montevideo, Uruguay
Paul Emsley, Cambridge, UK
Richard Garrat, São Carlos, Brazil
Ronan Keegan, Oxford, UK
Eugene Krissinel, Oxford, UK
Andrey Lebedev, Oxford, UK
Andrew Leslie, Cambridge, UK
Garib Murshudov, Cambridge, UK
Colin Palmer, Oxford, UK
James Parkhurst, Oxford, UK
Randy Read, Cambridge, UK
Clemens Vonrhein, Cambridge, UK 


Please find the program of the Workshop, the application form and further 
contact information, at http://pasteur.uy/mx2017 
(this www site will be updated regularly, so stay tuned!)

This Workshop is supported by the Collaborative Computational Project Nº4 
(CCP4, UK) & Science and Technology Facilities Council (UK); the Centro de 
Biologia Estructural del Mercosur (CeBEM); the International Union of 
Crystallography (IUCr); and the Institut Pasteur de Montevideo.

Organizers:
Alejandro Buschiazzo, PhD. Institut Pasteur de Montevideo, Uruguay
Ronan Keegan, PhD. CCP4, STFC Rutherford Appleton Laboratory, United Kingdom
Richard Garratt, PhD. Instituto de Fisica de Sao Carlos, USP, Brazil

Applicants:
24 students will be selected, aiming at advanced PhD, postdocs and young 
researchers. The Course will provide financial support covering registration 
fees, and for the case of those students coming from abroad, all local expenses 
(lodging, per diem and local transportation). Look in the www site for details 
on application procedures.

The application deadline is September 17, 2017.
 
Please address further inquiries to: mx2...@pasteur.edu.uy

Looking forward to welcoming you in Montevideo!

-- 
Alejandro Buschiazzo, PhD
Associate Professor
Laboratory of Molecular & Structural Microbiology
Institut Pasteur de Montevideo
Mataojo 2020
Montevideo 11400
URUGUAY
Phone: +598 25220910 int. 120
Fax:  +598 25224185
http://pasteur.uy/en/laboratorios-eng/microbiologia-estructural-y-molecular-eng

Re: [ccp4bb] Refienmnet

[Kay Diederichs]

Dear Rohit,

in your refinement table I find that the R-factors are elevated in the ice ring 
ranges (around 2.22 and 1.93 A resolution).
And your data collections statistics seem to confirm this -  CC1/2 is very high 
at high resolution which is often due to ice rings.

Could be a classical case of "data collection problem becomes visible at 
refinement stage".

best,

Kay

On Tue, 15 Aug 2017 22:09:44 +0530, rohit kumar  wrote:

>Dear All,
>
>
>
>I am refining a data in refmac5 and the data resolution is 1.8 A. Data is
>looking fine with the data statics see below for data statics
>
>
>
>[image: Inline image 1]
>
>
>
>Right now the R/Rfree is 22/26 not good for such resolution. I have tried
>most of the options in refmec5 but still I am not able to lower these
>R/Rfree values.
>
>During refinement with phenix what I found that at resolution 1.93 to 1.86
>R/Rfree is quite high see below
>
>
>[image: Inline image 2]
>
>
>
>
>Is this the possible reason for high R/Rfree value?. If it is  please let
>me know how some can remove these frames during refinement. or
>
>
>Please tell me other strategies to lower down the R/Rfree values.
>
>
>Thank you in advance
>
>
>With Regards
>
>Dr. Rohit Kumar Singh
>

Re: [ccp4bb] "reset" a structure before re-refinement

[Victor Lamzin]

Dear Graeme,
You can also type the following on a command line, optional commands are 
given in square parentheses.

Victor

$warpbin/arp_warp
mode shakemodel allatoms
files ccp4 xyzin FILENAME.pdb xyzout FILENAME.pdb
symmetry SPACEGROUP
shakemodel   [ bexclude B1 ] [ breset B1 B2 ] [ randomise X ] [ shift X 
Y Z ]

end


On 17/08/2017 17:17, Graeme Winter wrote:

Dear All,

Is there a protocol out there to gently perturb atomic positions so that re-running 
refinement can essentially put them back without bias from the original refinement? In 
particular, if trying to perform the Karplus and Diederichs paired refinement protocol, I 
do not want to run the lower resolution refinements with the "memory" of the 
weak high resolution data present... and only have the refined structure to work from...

Am using refmac5, but any pdb randomizer would hit the spot

Many thanks Graeme

[ccp4bb] postdoctoral position available

[Jeffrey B Bonanno]

I would like to draw your attention to a position available in New York City:

The laboratories of Kartik Chandran and Steve Almo at the Albert Einstein 
College of Medicine seek a highly motivated and innovative post-doctoral 
scientist interested in the structural, mechanistic and functional analysis of 
viral entry mechanisms exploited by New World and Old World Hantaviruses, and 
newly discovered emerging viruses. Albert Einstein offers a unique environment 
for these studies, including high-throughput resources for protein 
purification, biochemical studies, and high resolution structural analyses. 
Successful candidates must have demonstrated considerable expertise in protein 
chemistry and structural biology. This position requires a significant level of 
independence, as well as the ability to interface with a larger team of 
investigators, and will afford freedom in defining future courses of study.
 
Applicants must have a PhD, MD, or equivalent degree. Qualified applicants 
should submit a cover letter, curriculum vitae, and a brief summary of research 
accomplishments and goals in a single PDF document to steve.almo  
einstein.yu.edu. Applicants should also arrange to have three letters of 
reference sent directly to this email address.
 
cheers,
Jeff

Jeffrey Bonanno, Ph.D.
Department of Biochemistry
Albert Einstein College of Medicine
1300 Morris Park Avenue
Bronx, NY 10461
718-430-2452
jeffrey.bona...@einstein.yu.edu

Re: [ccp4bb] "reset" a structure before re-refinement

[George Sheldrick]

Dear Graeme,

The WIGL instruction in SHELXL does exactly that, and has some useful 
options.

http://shelx.uni-ac.gwdg.de/SHELX/shelxl_html.php#WIGL

Best wishes, George


On 08/17/2017 05:17 PM, Graeme Winter wrote:

Dear All,

Is there a protocol out there to gently perturb atomic positions so that re-running 
refinement can essentially put them back without bias from the original refinement? In 
particular, if trying to perform the Karplus and Diederichs paired refinement protocol, I 
do not want to run the lower resolution refinements with the "memory" of the 
weak high resolution data present... and only have the refined structure to work from...

Am using refmac5, but any pdb randomizer would hit the spot

Many thanks Graeme




--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or +49-5594-227312

Re: [ccp4bb] "reset" a structure before re-refinement

[Robbie Joosten]

In most cases resetting the B-factors would be enough to perturb the model.



Cheers,

Robbie



Sent from my Windows 10 phone



From: Andrew Leslie
Sent: 17 August 2017 17:29
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] "reset" a structure before re-refinement



Hi Graeme,

You can do this with PDBSET, keyword NOISE
Cheers,


Andrew

> On 17 Aug 2017, at 16:17, Graeme Winter  wrote:
>
> Dear All,
>
> Is there a protocol out there to gently perturb atomic positions so that 
> re-running refinement can essentially put them back without bias from the 
> original refinement? In particular, if trying to perform the Karplus and 
> Diederichs paired refinement protocol, I do not want to run the lower 
> resolution refinements with the "memory" of the weak high resolution data 
> present... and only have the refined structure to work from...
>
> Am using refmac5, but any pdb randomizer would hit the spot
>
> Many thanks Graeme
>
> --
> This e-mail and any attachments may contain confidential, copyright and or 
> privileged material, and are for the use of the intended addressee only. If 
> you are not the intended addressee or an authorised recipient of the 
> addressee please notify us of receipt by returning the e-mail and do not use, 
> copy, retain, distribute or disclose the information in or attached to the 
> e-mail.
> Any opinions expressed within this e-mail are those of the individual and not 
> necessarily of Diamond Light Source Ltd.
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any 
> attachments are free from viruses and we cannot accept liability for any 
> damage which you may sustain as a result of software viruses which may be 
> transmitted in or with the message.
> Diamond Light Source Limited (company no. 4375679). Registered in England and 
> Wales with its registered office at Diamond House, Harwell Science and 
> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

Re: [ccp4bb] "reset" a structure before re-refinement

[Andrew Leslie]

Hi Graeme,

You can do this with PDBSET, keyword NOISE
Cheers,


Andrew

> On 17 Aug 2017, at 16:17, Graeme Winter  wrote:
> 
> Dear All,
> 
> Is there a protocol out there to gently perturb atomic positions so that 
> re-running refinement can essentially put them back without bias from the 
> original refinement? In particular, if trying to perform the Karplus and 
> Diederichs paired refinement protocol, I do not want to run the lower 
> resolution refinements with the "memory" of the weak high resolution data 
> present... and only have the refined structure to work from...
> 
> Am using refmac5, but any pdb randomizer would hit the spot
> 
> Many thanks Graeme
> 
> -- 
> This e-mail and any attachments may contain confidential, copyright and or 
> privileged material, and are for the use of the intended addressee only. If 
> you are not the intended addressee or an authorised recipient of the 
> addressee please notify us of receipt by returning the e-mail and do not use, 
> copy, retain, distribute or disclose the information in or attached to the 
> e-mail.
> Any opinions expressed within this e-mail are those of the individual and not 
> necessarily of Diamond Light Source Ltd. 
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any 
> attachments are free from viruses and we cannot accept liability for any 
> damage which you may sustain as a result of software viruses which may be 
> transmitted in or with the message.
> Diamond Light Source Limited (company no. 4375679). Registered in England and 
> Wales with its registered office at Diamond House, Harwell Science and 
> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

[ccp4bb] "reset" a structure before re-refinement

[Graeme Winter]

Dear All,

Is there a protocol out there to gently perturb atomic positions so that 
re-running refinement can essentially put them back without bias from the 
original refinement? In particular, if trying to perform the Karplus and 
Diederichs paired refinement protocol, I do not want to run the lower 
resolution refinements with the "memory" of the weak high resolution data 
present... and only have the refined structure to work from...

Am using refmac5, but any pdb randomizer would hit the spot

Many thanks Graeme

-- 
This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

[ccp4bb] Assistant Professor position in Cryo-Electron Microscopy/Tomography at Princeton University

[Phil Jeffrey]

The Molecular Biology Department at Princeton University invites 
applications for a tenure-track faculty position at the Assistant 
Professor level.  We are seeking a colleague whose research will 
leverage high resolution cryo-electron microscopy and/or cryo-electron 
tomography in the study of outstanding biological questions. The 
successful candidate will join a friendly, highly collaborative faculty 
and will have access to superb resources including a new 300 kV Titan 
Krios TEM. We seek faculty members with a strong commitment to teaching, 
mentoring, and fostering a climate that embraces both excellence and 
diversity.


See the link: 
https://puwebp.princeton.edu/AcadHire/apply/application.xhtml?listingId=2821


Applications must be received by October 31, 2017.

Note: I'm just the messenger and not involved at all in the search process.


Phil Jeffrey
Macromolecular crystallography facility manager
Princeton

[ccp4bb] Postdoctoral position - Group of Professor Gabriel Waksman - Birkbeck

[Gabriel Waksman]

Postdoctoral Researcher – Cryo-Electron Microscopy and Cell Biology of Type IV 
Secretion Systems

The ISMB at Birkbeck is seeking one Post-doctoral Research Assistant to carry 
out structural and cellular analysis of the Type IV Secretion Systems by 
cryo-electron tomography, cryo-electron microscopy, and fluorescence imaging 
microscopy with Professor Gabriel Waksman. The laboratory has been 
exceptionally productive over the years in this area (see Science, 2009, 
323:266-268; Nature, 2009, 462:1011-1015; Nature. 2014, 508:550-3; Cell. 2016, 
166, 1436–1444; and Cell. 2017, 169, 708–721). The research programme is funded 
by a grant from the Wellcome Trust. Further details on the research group and 
on type IV secretion can be found at 
http://www.ismb.lon.ac.uk/gabriel-waksman/homepage.htm.

Applicants should have a PhD in Structural Molecular Biology, and experience in 
Electron Microscopy, Image Processing, Biophysics or related areas.

Salary: Grade 7 of the College's London Pay Scale which is £36,548 rising to 
£41,772 per annum. The closing date for completed applications is midnight on 
30 September 2017. Interviews will be held on Tuesday 17 October 2017.