Dear all,
Regarding the job submission in SLURM from CCP4i, I wanted to add that it is
possible for ARCIMBOLDO jobs to do it directly from the interface, you need to
specify the path to a configuration file containing the required informations.
More info on this configuration file are found here:
http://chango.ibmb.csic.es/installation
If you need any help for the configuration you can write back to me anytime.
Best wishes,
Massimo Sammito
> Il giorno 07 apr 2017, alle ore 01:01, CCP4BB automatic digest system
> <lists...@jiscmail.ac.uk> ha scritto:
>
> There are 7 messages totaling 992 lines in this issue.
>
> Topics of the day:
>
> 1. ccp4/coot on macOSSierra (3)
> 2. How to submit to SLURM from CCP4i
> 3. suggestion on protein crystallization optimization from phase separation
> 4. Post-doc in membrane protein structural biology, Pfizer Inc
> 5. Reminder: Structural biologist in metabolic diseases, SGC University of
> Oxford
>
> ----------------------------------------------------------------------
>
> Date: Thu, 6 Apr 2017 08:59:24 +0000
> From: "POHL, EHMKE" <ehmke.p...@durham.ac.uk>
> Subject: ccp4/coot on macOSSierra
>
> Dear ccp4 community,
>
> I would appreciate any suggestions how to get the ccp4 interfaces (ccp4 and
> ccp4i2) and coot running on the new MacBook Pro under macOS Sierra 10.12.3.
> control. I have already tried different Xquartz version with no success
>
> thanks so much
>
> Ehmke
>
> ------------------------------
>
> Date: Thu, 6 Apr 2017 10:52:47 +0100
> From: Nikos Pinotsis <n.pinot...@mail.cryst.bbk.ac.uk>
> Subject: Re: ccp4/coot on macOSSierra
>
> Hi Ehmke,
>
> for sierra 10.12.3 try with the Xquartz 2.7.9 (xorg-server 1.17.4). This
> set up works for me (including pymol etc)
>
> good luck
>
> Nikos
>
> Dr. Nikos Pinotsis
> Institute of Structural and Molecular Biology
> Department of Biological Sciences, 3rd Floor, R313
> Birkbeck College
> Malet Street
> London WC1E 7HX
> T: +44 (0)207 631 6827
> F: +44 (0)207 631 6803
> M: +44 (0)792 384 3593
>
>> On 06/04/2017 09:59, POHL, EHMKE wrote:
>> Dear ccp4 community,
>>
>> I would appreciate any suggestions how to get the ccp4 interfaces
>> (ccp4 and ccp4i2) and coot running on the new MacBook Pro under macOS
>> Sierra 10.12.3. control. I have already tried different Xquartz
>> version with no success
>>
>> thanks so much
>>
>> Ehmke
>
> ------------------------------
>
> Date: Thu, 6 Apr 2017 11:56:57 +0200
> From: Didier Spittler <spittlerdid...@gmail.com>
> Subject: Re: ccp4/coot on macOSSierra
>
> Hello Nikos,
>
> I use Zquartz 2.7.9 too and it works fine for me.
>
> Best,
>
> Didier
>
> 2017-04-06 11:52 GMT+02:00 Nikos Pinotsis <n.pinot...@mail.cryst.bbk.ac.uk>:
>
>> Hi Ehmke,
>>
>> for sierra 10.12.3 try with the Xquartz 2.7.9 (xorg-server 1.17.4). This
>> set up works for me (including pymol etc)
>>
>> good luck
>>
>> Nikos
>>
>> Dr. Nikos Pinotsis
>> Institute of Structural and Molecular Biology
>> Department of Biological Sciences, 3rd Floor, R313
>> Birkbeck College
>> Malet Street
>> London WC1E 7HX
>> T: +44 (0)207 631 6827 <+44%2020%207631%206827>
>> F: +44 (0)207 631 6803 <+44%2020%207631%206803>
>> M: +44 (0)792 384 3593 <+44%207923%20843593>
>>
>> On 06/04/2017 09:59, POHL, EHMKE wrote:
>>
>> Dear ccp4 community,
>>
>> I would appreciate any suggestions how to get the ccp4 interfaces (ccp4
>> and ccp4i2) and coot running on the new MacBook Pro under macOS Sierra
>> 10.12.3. control. I have already tried different Xquartz version with no
>> success
>>
>> thanks so much
>>
>> Ehmke
>>
>>
>>
>
>
> --
> Didier Spittler, PhD
> Phone number : +33658576481
>
> ------------------------------
>
> Date: Thu, 6 Apr 2017 14:31:35 +0200
> From: Jesper Lykkegaard Karlsen <je...@mbg.au.dk>
> Subject: How to submit to SLURM from CCP4i
>
> #!/bin/bash
> #
> # Simple script for submitting ccp4i jobs to the SLURM queuing system
> # Hack inspired from the ccp4i_condorsub script by Ronan Keegan
> #
> # Jesper Lykkegaard Karlsen 06/04/2017
> #
>
> # Takes the ccp4i job com file as input
> infile=$2
>
> # Get the def file location, name and the job number
> def_file_line=`grep \.def $infile`
> def_file=${def_file_line##*-r}
> def_file_name=${def_file##*/}
> job_number_name=${def_file_name%.*}
>
> # Define and make scratch dir on remote FS
> CCP4_REM_SCR=$HOME/.ccp4_rem_scr
> if [ ! -d $CCP4_REM_SCR ]; then
> mkdir $CCP4_REM_SCR
> fi
>
> # Move def_file to CCP4_REM_SRC and define new var
> cp -a $def_file $CCP4_REM_SCR/
>
> # Get the project name from the def file
> project_line=`grep CCP4I $def_file | grep PROJECT `
> project=${project_line##* }
>
> # Create the condor submission script
> cat << eof > ${CCP4_REM_SCR}/${job_number_name}_${project}_sbatch.sub
> #!/bin/bash
> #SBATCH -N1
> #SBATCH --share
> #SBATCH -o ${CCP4_REM_SCR}/${job_number_name}_${project}_sbatch.out
>
> source /etc/profile.d/modules.sh
> module load ccp4-7.0
>
> ${CCP4}/bin/ccp4ish -r ${CCP4_REM_SCR}/${def_file_name}
>
> eof
>
> # Submit the job to the Sbatch queue
> sbatch ${CCP4_REM_SCR}/${job_number_name}_${pro
>
> ------------------------------
>
> Date: Thu, 6 Apr 2017 23:16:26 +0800
> From: Joseph Ho <sbddintai...@gmail.com>
> Subject: suggestion on protein crystallization optimization from phase
> separation
>
> Dear all:
>
> I would like to seek your suggestion on protein crystallization from
> phase separation.
> We recently observed many small round droplets shown in our
> protein/DNA crystallization. Condition are 0.8M-1.6M LiSO4; 20mM
> MgCl2; pH 5-8; protein conc. ~15mg/ml). The UV microscope confirms
> those are protein-rich phase separation.
> We have tried to change conc. of LiSO4 and pH. Still we got different
> size and amount of small round droplets. At 20 degree, those droplets
> appear within one day and at 4 degree, it takes two-three days. We
> also tried additive and silver bullet screen. So far, we have not
> found a condition to have protein crystals. The protein is already
> truncated. Several DNA constructs are on-going.
> At this point, I would like to seek your advice on the method to
> optimize the condition. Based on
>
>
> PS. Any people have luck with protein crystallization by streaking the
> Gelationous protein to new drop as shown in
> http://xray.bmc.uu.se/terese/tutorial3.html . Can you please share
> your experience with us?
>
> Thanks for your help.
>
> Joseph Ho
>
> ------------------------------
>
> Date: Thu, 6 Apr 2017 15:39:12 +0000
> From: "Liu, Shenping" <shenping....@pfizer.com>
> Subject: Post-doc in membrane protein structural biology, Pfizer Inc
>
> Post-doc Fellow position in membrane protein structural biology at Pfizer
> Inc. Job id #: 1051468. To apply, click on link below.
>
> https://www.linkedin.com/jobs/view/290461069?trk=jobs-home-jobsfe-redirect).
>
> For people without Linkedin account, please apply using link below with Job
> id #1051468
> https://globaljobs.pfizer.com/pages/job-details.aspx
>
>
> Shenping Liu, PhD
> Associate Research Fellow
> Pfizer Groton Labs, CT, USA
>
> Postdoctoral Fellow position at Pfizer focused on membrane protein
> structure-function studies
>
> We are seeking a highly qualified and energetic PhD scientist to join us as a
> postdoctoral researcher focused on elucidating the three dimensional
> structures of membrane proteins that serve as important drug transporters.
> The incumbent will be trained in the state-of-the-art science of membrane
> protein structural biology, be exposed to the drug discovery and development
> process, and will learn the application of structure information in drug
> design. At our disposal, we have extensive in-house experience and
> resources supporting protein expression, purification, crystallization,
> structure determination of both soluble and membrane-bound proteins.
> Presently, Pfizer scientists have regular access to all the major X-ray
> synchrotron beam lines in the world, in house Cryo-EM facilities, and rich
> collection of small molecular ligands to enable protein stabilization and
> crystallization. Ideal candidates should have experience in protein
> expression, protein purification and crystallography, and preferably less
> than 4 years postdoctoral experience.
>
> Pfizer Inc
> Founded in 1849, Pfizer is the world's premier biopharmaceutical company. We
> discover, develop, manufacture and deliver quality, safe and effective
> prescription medicines to treat and help prevent disease for both people and
> animals. We also partner with healthcare providers, governments and local
> communities around the world to expand access to our medicines and to provide
> better quality health care and health system support.
>
> Job Focus
> The postdoctoral fellow will join the Structural and Molecular Sciences group
> based in Groton CT, a multidisciplinary group that is well-established and
> recognized for its leadership in structural biology of both soluble and
> membrane proteins.
>
> In this exciting and cross-disciplinary project, we aim to elucidate three
> dimensional structures of membrane proteins involved in drug transportation.
> Specifically, this research determines three dimensional structures of drug
> transporters and addresses the need of understanding structure-function
> relationship.
>
> The incumbent is expected to work closely with fellow scientists across many
> other disciplines, deliver the results internally and externally via meeting
> presentations and publications.
>
> Responsibilities
> Optimize membrane protein constructs for functional expression and protein
> stability.
> Purification of functional membrane proteins for structural determinations.
> Protein crystallization and data collection. Sample preparation for Cryo-EM
> and data collection. Data analysis and structure determination. Structure
> analysis to understand structure-function relationship.
> Interface with scientists across lines/discipline and show strong initiative
> in developing ideas to assist in the design of exploratory experiments.
> Collect up-to-date information and keep abreast of the relevant literature,
> data acquisition and analysis, manuscript preparation, presentation of study
> results in oral and poster formats.
>
> Qualifications
> Ph.D. in structural biology with extensive knowledge in molecular biology,
> protein chemistry and wet lab protein structural biology skills.
> Previous experience with protein construct design, expression and
> purification is required.
> Previous experience with membrane protein is a plus.
> Previous experience in structure determination is a plus.
> Demonstrated track record of publishing in peer-reviewed scientific journals.
> Excellent communication skills and ability to work independently are
> essential.
>
> ------------------------------
>
> Date: Thu, 6 Apr 2017 18:15:53 +0100
> From: "Wyatt W. Yue" <yuewai...@gmail.com>
> Subject: Reminder: Structural biologist in metabolic diseases, SGC University
> of Oxford
>
> Dear all,
>
> A reminder of the below job opening at SGC University of Oxford.
> We are looking for an enthusiastic structural biologist with experience in
> drug discovery.
> Deadline in a week's time (13th April 12pm GMT+1)
>
> Wyatt Yue
>
>> On 15 March 2017 at 12:32, Wyatt W. Yue <yuewai...@gmail.com> wrote:
>>
>> Dear all
>>
>> We are recruiting a structural biologist at senior/postdoctoral level, to
>> join the metabolic research team at the SGC University of Oxford, led by
>> Assoc Prof Wyatt Yue.
>>
>> You will be part of a dynamic and focused team, elucidating the molecular
>> mechanism and small molecule therapy for the causative gene products of
>> common (e.g. diabetes, obesity, endocrinology) and rare (e.g. inborn errors
>> of metabolism) disorders.
>>
>>
>> - You have a PhD in structural biology/biochemistry
>> - You have experience in structure-based drug discovery
>> - You have interest in the field of metabolic diseases
>> - You are a self-starter, team player and completer/finisher who
>> enjoys a challenge
>>
>> Interested applicants please refer to job description and apply online via
>> the page (Vacancy ID: 127848):
>>
>> https://www.ndm.ox.ac.uk/current-job-vacancies/vacancy/
>> 127848-Structural-Biologist-in-Metabolic-and-Rare-Diseases
>>
>>
>>
>> Closing date: *12.00 midday (UK) on Thursday 13 April 2017*
>>
>>
>> Informal enquiries to wyatt....@sgc.ox.ac.uk
>>
>> Visit Wyatt Yue’s SGC home page: http://www.thesgc.org/wyatt
>>
>
> ------------------------------
>
> End of CCP4BB Digest - 5 Apr 2017 to 6 Apr 2017 (#2017-95)
> **********************************************************
