[ccp4bb] Imperial College London - Postdoctoral Research Fellow position - X-ray crystallography

[Cota Segura, Ernesto]

Postdoctoral Research Fellow position at Imperial College London

We are seeking an outstanding structural biologist to contribute to an ongoing 
drug discovery project in the groups of Dr Ernesto Cota (Department of Life 
Sciences) and Prof Edward Tate (Department of Chemistry), funded by Cancer 
Research UK. This project focuses on structure-guided design of ligands against 
small GTPases, a validated but challenging set of targets. The project is 
supported by collaborations with structural, cell biologists, medicinal 
chemists at Imperial and the CRUK Beatson Institute (Glasgow).

Our research is backed by a robust combination of biophysical, biochemical and 
cellular assays. You will be expected to take a leading role in fragment-based 
screening, in silico design, protein X-ray crystallography, protein- and 
ligand-based NMR, and biophysical (ITC, SPR, MST) and biochemical assays, 
integrating data generated by colleagues working on hit optimisation and 
hit-to-lead programmes using medicinal chemistry approaches.

For further information, please click this 
link

Best wishes,
Ernesto


Dr Ernesto Cota
Senior Lecturer

Imperial College London
Department of Life Sciences
Room 601, Sir Ernst Chain (Biochemistry) Building
Exhibition Rd., South Kensington
London SW7 2AZ






To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] How to fix residual B value problem in pdbredo

[Robbie Joosten]

Hi Kahkashan,

Thanks for your faith in pdb-redo. I'm glad you are happy with the results. If 
you download the zip file with all output, there is a file called 
_final_tot.pdb this one has the total B-factors as ANISOU records.

Cheers,
Robbie

On 16 Aug 2018 18:11, Firdous Tarique  wrote:

Hello everyone

I have a structure whose quality improves a lot when submitting it to PDB-Redo 
server. But when I am trying to put the output coordinates for validation it is 
not taking up and comes with message that: Structure contains Residual B values 
and TLS records are present but required ANISOU records are missing.

I don't want to play with the refinement anymore and want to use the output 
from the PDB-Redo for validation and deposition.

Is their anyway to incorporate residual B values and ANISOU record without 
doing much change to the refinement statistics.


Regards

Kahkashan



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] How to fix residual B value problem in pdbredo

[Firdous Tarique]

*Hello everyoneI have a structure whose quality improves a lot when
submitting it to PDB-Redo server. But when I am trying to put the output
coordinates for validation it is not taking up and comes with message that:
Structure contains Residual B values and TLS records are present but
required ANISOU records are missing.I don't want to play with the
refinement anymore and want to use the output from the PDB-Redo for
validation and deposition. Is their anyway to incorporate residual B values
and ANISOU record without doing much change to the refinement
statistics.RegardsKahkashan *



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Coot: Failed to load module

[nic steussy]

All,

I am having difficulty running Coot through my ccp4 install since I 
upgraded to Ubuntu 18.04 (MATE variant).  The error:


 steussy@osprey:~$ coot
Gtk-Message: Failed to load module "gail"
Gtk-Message: Failed to load module "atk-bridge"
Gtk-Message: Failed to load module "gail"
Gtk-Message: Failed to load module "atk-bridge"
Gtk-Message: Failed to load module "canberra-gtk-module"
Gtk-Message: Failed to load module "canberra-gtk-module"
Gtk-Message: Failed to load module "topmenu-gtk-module"
/usr/local/ccp4-7.0/bin/coot: line 292: 11480 Segmentation fault  
(core dumped) $coot_bin "$@"


Coot runs fine if I run it as root.  So I'm guessing it is a permission 
problem somewhere.


Things I've tried:
Reinstallation of CCP4/Coot
changing ownership of the ccp4-7.0 directory tree from root to me.
review of all the associated libraries to assure proper ownership and 
permissions.


If anyone has a clue it would be appreciated.

Nic out


--

C. Nicklaus Steussy, M.D., Ph.D.
Purdue University
csteu...@purdue.edu




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Post-doc and PhD student positions available in Poznan

[Mirek Gilski]

Dear All,
I'd like to draw your attention to the openings for Post-doc at Center 
for Biocrystallographic Research (Poznan, Poland),
to work on a combination of protein crystallography and supramolecular 
chemistry.


The project overview can be found at: 
http://www.man.poznan.pl/CBB/JOBS/POF.pdf
and the offer description at: 
https://drive.google.com/file/d/1XyY6AeSKYjmppym2F8dDthIy-OASjx2K/view?usp=sharing


The deadline for applications is *08th September 2018.
*
I would be grateful if you could forward this opportunity to potential 
applicants.


Kind regards and all best wishes,
Mirek Gilski
p.s.
We also have an open position for PhD student in our lab, deadline: 31 
August 2018. Interested people please contact me directly (ASAP).




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Senior Research Investigator at Bristol-Myers Squibb in X-ray crystallography and cryo-EM

[Sheriff, Steven]

All:

Bristol-Myers Squibb has an open Ph.D. level position in X-ray crystallography 
and cryo-EM. The only way to apply for this position is through the following 
web site:

* 
https://bristolmyerssquibb.wd5.myworkdayjobs.com/BMS/job/Princeton---NJ---US/Senior-Research-Investigator_R1508425-1

[Questions or issues with the web site, please contact 
michael.kush...@bms.com, Talent Acquisition 
Specialist, R]

Bristol-Myers Squibb is a global biopharmaceutical company whose mission is to 
discover, develop and deliver innovative medicines that help patients prevail 
over serious diseases.

One shared journey is moving us forward at Bristol-Myers Squibb. Around the 
world, we are passionate about making an impact on the lives of patients with 
serious disease. Empowered to apply our individual talents and ideas so that we 
can learn and grow together.  Driven to make a difference, from innovative 
research to hands-on community support.  Bristol-Myers Squibb recognizes the 
importance of balance and flexibility in our work environment. We offer a wide 
variety of competitive benefits, services and programs that provide our 
employees the resources to pursue their goals, both at work and in their 
personal lives.

As a key member of the Molecular Structure & Design group, the successful 
candidate will be required to have knowledge of and experience in all 
structural biology techniques including construct design, expression, 
purification, characterization, crystallization, structure determination and 
analysis.  Strong skills in both X-ray crystallography and single particle 
cryoEM is required.  The new group member will be involved in early stages of 
drug discovery programs which requires close collaboration with molecular 
biologists, protein scientists and structural biologists as well as biologists 
and chemists working in the various disease biology and translational areas 
within preclinical research. The candidate must be self-motivated, possess 
excellent communication skills, and work both independently as well as in 
teams. Personal attributes of integrity and scientific creativity are required.

Major Skills and Experience Preferred:
oRecombinant protein construct design
oProtein expression and purification
oX-Ray crystallography
oSingle particle cryoEM
oStructure analysis
Experience:
o4-6 years post Ph.D. experience
oPh.D. qualification


This message (including any attachments) may contain confidential, proprietary, 
privileged and/or private information. The information is intended to be for 
the use of the individual or entity designated above. If you are not the 
intended recipient of this message, please notify the sender immediately, and 
delete the message and any attachments. Any disclosure, reproduction, 
distribution or other use of this message or any attachments by an individual 
or entity other than the intended recipient is prohibited.



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] crystals that dont diffract :( :(

[Patrick Shaw Stewart]

Hi Careina

Expanding on what Tim says, try crushing your crystals to make a seed
stock, and adding it to a few *random screens - *preferably screens that
you have already tried with this target.

Search for instructions for MMS or rMMS online.

Good luck,

Patrick



On 14 August 2018 at 11:34, Tim Gruene  wrote:

> Dear Careina,
>
> you could use the old crystals, that did not diffract, for microseeding
> to regrew nicer crystals. Once you have them, try to use them as quickly
> as possible. Three weeks can be a long time for crystals.
>
> Storage in liquid nitrogen should not be the problem.
>
> Best,
> Tim
>
>
> On 08/14/2018 11:58 AM, Careina Edgooms wrote:
> > I got the most beautiful crystals I have ever seen and they don't
> > diffract at all. Not poor diffraction, NO diffraction. Anyone know why
> > this could be and how I can go about fixing it? I had three beautiful
> > crystals and not one diffracted. I did leave them in the drop for about
> > 3 weeks before harvesting and in liquid nitrogen for about a month
> > before diffracting. Could that be a factor? If I regrew more beautiful
> > crystals and diffracted straight away could that help?
> > Careina
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> >
>
> --
> --
> Paul Scherrer Institut
> Tim Gruene
> - persoenlich -
> OSUA/204
> CH-5232 Villigen PSI
> phone: +41 (0)56 310 5297
>
> GPG Key ID = A46BEE1A
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



-- 
 patr...@douglas.co.ukDouglas Instruments Ltd.
 Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
 Directors: Peter Baldock, Patrick Shaw Stewart

 http://www.douglas.co.uk
 Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
 Regd. England 2177994, VAT Reg. GB 480 7371 36



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] Fishing crystals from volatile solvent as precipitant

[Patrick Shaw Stewart]

Hi Thomas

One problem with conventional approaches is that you tend to get high
mosaicity when harvesting from drops with isopropanol.

A very good method, invented by my old friend Lesley Haire, that has always
worked (so far!) is to use microbatch-under-oil with a plate called the
Vapor Batch plate.

   - Set up the drops with everything in them except for the isopropanol.


   - Cover the drops with 50:50 paraffin and silicone oil ("Al's Oil").


   - Put a few mL of 27% isopropanol in the "moat" around the outside of
   the plate.


The isopropanol will saturate the oil and then diffuse into the drops.  You
can take your time and harvest the crystals through the oil. The oil
protects the crystals, preventing evaporation of isopropanol.

Let me know if you (or anyone) would like some sample plates to try this
out.

See example and ref. below.

Best wishes, Patrick

___


Example: https://www.douglas.co.uk/winner1.htm

*G. B. Mortuza et al.. High-resolution structure of a retroviral capsid
hexameric amino-terminal domain.  Nature 431 (2004), pp 481-485. (This
paper describes the use of the vapor batch plate with isopropanol.)*

Sent from mobile

Patrick Shaw Stewart
+44 7901 548 201

On Wed, 15 Aug 2018, 08:41 Yvonne Thielmann,  wrote:

> Dear Thomas,
>
> maybe you can try to overlay your drop with LV CryoOil from Jena
> Bioscience. Then the evaporation of the solvent is slowed down and the
> crystals are directly cryoprotected when you move the crystals through
> the oil. We had quite good results when we cryoprotected crystals in
> this oil.
>
> Best wishes,
> Yvonne
>
>
> --
> Dr. Yvonne Thielmann
> Max Planck Institute of Biophysics
> Molecular Membrane Biology
> Max-von-Laue-Strasse 3
> 60438 Frankfurt / Main
> Germany
>
> Office +49 69 6303 1056
> Lab +49 69 6303 1074
> Fax +49 69 6303 1002
>
> Am 15.08.2018 um 08:05 schrieb Kajander, Tommi A:
> > Yes sorry, i meant paratone-N also.
> >
> > Tommi
> >
> > Kohteesta: ferrer
> > Lähetetty: keskiviikko 15. elokuuta klo 0.41
> > Aihe: Re: [ccp4bb] Fishing crystals from volatile solvent as precipitant
> > Vastaanottaja: ccp4bb@jiscmail.ac.uk
> >
> >
> > Dear Thomas,
> >
> > Alternatively you can try shooting on crystals in the drop, in situ. So
> > fishing, no cryo. But potentially high radiation damage. Can be
> > considered if you have enough crystals, and if your crystallization
> > plate makes it possible.
> >
> > Regards
> >
> > JL
> >
> > On 14/08/2018 20:58, Thomas Krey wrote:
> > Dear crystallization experts,
> >
> > We have 3D protein crystals grown from a microseed matrix screening
> > vapor diffusion experiment in either
> >
> > 15% (v/v) Reagent alcohol
> > HEPES Na pH 7.5
> > 0.2 M MgCl2
> >
> > or in
> >
> > 27% Isopropanol
> > 0.18 M MgCl2
> > 90 mM HEPES Na pH 7.5
> > 10% Glycerol
> >
> > Upon opening the corresponding wells these crystals move quite a bit –
> > presumably due to the volatility of the alcohols. Does anyone have a
> > good suggestion to stabilize the swirling movements? Does anyone have
> > experience, whether these conditions alone can serve as cryo-protectant
> > (i.e., do we really have to fish, move into cryo solution and fish
> again)?
> > Any suggestion or input would be highly welcome.
> >
> > Thank you very much in advance.
> >
> > Thomas
> >
> >
> > Prof. Dr. Thomas Krey
> > Hannover Medical School
> > Institute of Virology
> > Structural Virology Group
> > Carl-Neuberg-Str. 1
> > D-30625 Hannover
> > phone: +49 (0) 511 - 532 4308
> > email: krey.tho...@mh-hannover.de 
> >
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> >
> > --  Jean-Luc Ferrer Institut de
> Biologie
> > Structurale 71 Avenue des Martyrs CS 10090 38044 Grenoble Cedex 9 -
> > FRANCE Ph.: +33 (0)4 57 42 85 22 Cell: +33 (0)6 89 45 13 57 email:
> > jean-luc.fer...@ibs.fr 
> > 
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> >
> >
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> >
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1