[ccp4bb] Postdoctoral position at the University of Chicago

[Robert Keenan]

The Keenan lab at the University of Chicago has an opening for a postdoctoral 
scientist to study the structure and function of protein complexes involved in 
membrane protein biogenesis and quality control. 

Applicants should be nearing completion of a PhD in structural biology and have 
a strong academic record with significant publications. Experience in molecular 
biology, protein purification and electron microscopy/x-ray crystallography is 
required. 

To apply, please send a CV and a short statement describing your motivation for 
wanting to join the lab. Please be prepared to arrange for three letters of 
reference to be sent by email. 

For more information, please visit our webpage:  
http://keenanlab.bsd.uchicago.edu 

Re: [ccp4bb] Refienmnet

[Dale Tronrud]

   Your first step is to look at your images and see what is going on in
that shell.  Since you are looking at merged stats the first guess is
that there is something wrong with all of the images, but only by
looking at them can you tell.

Dale Tronrud

On 8/15/2017 9:39 AM, 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
> 
>  
> 
> 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 
> 
> 
> 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
> 
> 

[ccp4bb] An open postdoctoral position in structural enzymology at the University of Kentucky

[Oleg Tsodikov]

A postdoctoral position is available in the laboratory of Dr.
Oleg Tsodikov at the University of Kentucky, Department of
Pharmaceutical Sciences starting in early 2018 or later, to perform
structural, biochemical and biophysical studies of proteins involved in
bacterial drug resistance. We seek highly motivated individuals with a
Ph.D. degree and with experience in protein purification and
enzymatic assays.

Applicants should email Dr. Oleg Tsodikov at ovts...@uky.edu.
Please, include a CV and contact information for 3 references.

Re: [ccp4bb] [phenixbb] Opening phenix X-ray/neutron maps in Coot without the Phenix GUI

[Derek Logan]

Hi Paul,

Thanks, that was fast! There was a small typo in the phase column labels, which 
I've fixed in the attached file. Otherwise it works very well. Great that it 
opens the most recently-created MTZ file by default. I'll test the other option 
in due course.

/Derek


On 15 Aug 2017, at 14:36, Paul Emsley 
mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:


Hi Derek,

I have attached a script.  Drop it in your ~/.coot-preferences directory and 
restart your Coot. Should work (not tested).  If you want a specific mtz file, 
then you will have to use x-n-open via Calculate -> Scripting -> Scheme.

Paul.




xray-neutron.scm
Description: xray-neutron.scm

Re: [ccp4bb] [phenixbb] Opening phenix X-ray/neutron maps in Coot without the Phenix GUI

[Paul Emsley]

Hi Derek,

I have attached a script.  Drop it in your ~/.coot-preferences directory and restart your Coot. Should work 
(not tested).  If you want a specific mtz file, then you will have to use x-n-open via Calculate -> 
Scripting -> Scheme.


Paul.

;; return a list of map numbers
(define (x-n-open mtz-file-name)

  (map (lambda (col-pair)
 (make-and-draw-map mtz-file-name (car col-pair) (cadr col-pair) "" 0 
(caddr col-pair)))
   (list 
(list "2FOFCWT_xray""PH2FOFCWT_xray"0)
(list  "FOFCWT_xray"   "FOFCWT_xray"1)
(list "2FOFCWT_neutron" "PH2FOFCWT_neutron" 0)
(list  "FOFCWT_neutron""FOFCWT_neutron" 1

(if (defined? 'coot-main-menubar)
(let ((menu (coot-menubar-menu "Neutron")))
  (add-simple-coot-menu-menuitem 
   menu "Quick-load MTZ"
   (lambda () (x-n-open (most-recently-created-file "*.mtz" "."))

[ccp4bb] Reminder: PSI / CCP4 Workshop "3D Electron Crystallography for Macromolecular Compounds"

[Tim Gruene]

Dear all,

this is a reminder of the PSI / CCP4 Workshop 

"3D Electron Crystallography for Macromolecular Compounds"

The workshop will take place at PSI between 18th and 22nd September 2017.

Please see the full program, list of speakers, and registration instructions 
at 
https://indico.psi.ch/conferenceDisplay.py?confId=5525

We extended the number of participants by 10 places. 

Please register before 1st September 2017.

On behalf of the organisers,
Tim Gruene
-- 
--
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
Principal Investigator
Biology and Chemistry
OFLC/104
CH-5232 Villigen PSI

Phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A



signature.asc
Description: This is a digitally signed message part.

Re: [ccp4bb] Opening phenix X-ray/neutron maps in Coot without the Phenix GUI

[Paul Emsley]

On 15/08/2017 12:52, Derek Logan wrote:
Hi ccp4bb 

Is there a convenient way to open MTZ files in Coot that are the result of joint X-ray/neutron refinement in 
phenix.refine, but where phenix.refine was run in command-line mode? I would like achieve what is done in 
the Phenix GUI at the click of a button, i.e. open Coot with the structure and 2Fo-Fc and Fo-Fc maps for 
both neutron and X-ray. 


There is no button for this, but you can make one with a bit of scripting.

Paul.

[ccp4bb] Opening phenix X-ray/neutron maps in Coot without the Phenix GUI

[Derek Logan]

Hi ccp4bb and phenixbb,

Is there a convenient way to open MTZ files in Coot that are the result of 
joint X-ray/neutron refinement in phenix.refine, but where phenix.refine was 
run in command-line mode? I would like achieve what is done in the Phenix GUI 
at the click of a button, i.e. open Coot with the structure and 2Fo-Fc and 
Fo-Fc maps for both neutron and X-ray. At the moment I have to open each MTZ 
file four times in the Coot GUI, once for each type of map. Is there a script 
buried somewhere in the Phenix installation that can be modified?

/Derek

Derek Logan tel: +46 46 222 1443
Associate Professor mob: +46 76 8585 707
Dept. of Biochemistry and Structural Biology  
www.cmps.lu.se
Centre for Molecular Protein Science  bit.ly/2d0HxmS
Lund University, Box 124, 221 00 Lund, Sweden

[ccp4bb] Application deadline approaching: In Situ Serial Crystallography Workshop at SLS

[Vincent Olieric]

*In Situ Serial Crystallography - ISSX2 Workshop*

http://indico.psi.ch/event/ISSX2

*Swiss Light Source, Paul Scherrer Institute, Switzerland*
*Nov. 27-29, 2017*

*The application deadline is Sept 1*.


The *In Situ* Serial Crystallography Workshop ISSX2 is dedicated to the
presentation of the *in meso in situ serial crystallography (IMISX)* method
(Huang et al. 2016 ActaD) for the *X-ray structure determination of
membrane proteins*.

The workshop consists of introductory lectures, as well as presentations of
serial crystallography activities at both synchrotron and XFEL facilities.
The main part of the workshop focuses on hands-on practicals on methods for
growing crystals of membrane proteins by the *in meso* or lipidic cubic
phase (LCP) method, for collecting serial diffraction data on
micro-crystals directly *in situ* and for processing the data most
efficiently for high-resolution structure determination.

There is no registration fee and all local expenses will be covered, but
participants are requested to take care of their travel arrangements. The
workshop is limited to 20 students.

*Organizers*
Vincent Olieric (PSI), Meitian Wang (PSI), Martin Caffrey (Trinity College
Dublin), Kay Diederichs (University of Constance)
http://indico.psi.ch/event/ISSX2