Re: [ccp4bb] Help with omit map

[Pavel Afonine]

As others suggested, you can use Polder map:

- how-to video tutorial can be found here:

http://www.phenix-online.org/documentation/reference/tutorial_channel.html

- background is described here:

http://journals.iucr.org/d/issues/2017/02/00/ba5254/ba5254.pdf

Pavel


On Tue, Jul 24, 2018 at 3:26 PM, Vikram Dalal 
wrote:

> Hi everyone,
>
>
> I have to generate the omit map of metal and coordinating residues of
> protein structure for the figure.
>
> Which program can be used to generate the omit map for my requirement.
>
>
>
> Thanks & Regards,
>
>
>
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] Position Available: HPC and Data-Processing Specialist (Campinas, Brazil)

[Marin van Heel]

POSITION AVAILABLE:

HPC and Data-Processing Specialist (Campinas, Brazil)

LNNano, CNPEM Campinas / São Paulo, Brazil.

General job description

- Support of HPC clusters and massive data storage, including: user 
support, installation and maintenance of programmes and libraries, 
participation in ongoing research and software development projects.
- Provide training for internal/external users of our National Facility 
in using the HPC clusters and available programmes. Writing /maintaining 
user manuals.
- Daily operation of the HPC clusters ( licences, repairs, contacts with 
hardware/software providers.
- Supporting LNNano’s general IT activities and formulating policies (in 
conjunction with LNNano directors and the CNPEM general IT support group).
- Providing support for meetings, courses, supporting WEB-site, and 
participating in dissemination activities of our HPC -elated scientific 
results.


Qualification requirements

- PhD in Computational Science, Computer engineering, Physics, 
Chemistry, Structural Biology, or related areas.
- Experience in (parallel) programing in languages such as: C, C++; 
FORTRAN, CUDA, Python.

- Post-doctoral research experience is an advantage
- Experience in system-management of Linux OS environments.
- English language proficiency

Please send your CV and salary inquiries to: mariana.stevana...@cnpem.br 
, subject line:  “142376”


==

Cheers

Marin

--
==

    Prof Dr Ir Marin van Heel

    Laboratório Nacional de Nanotecnologia - LNNano
    CNPEM/LNNano, Campinas, Brazil

    tel:    +55-19-3518-2316
  Skype:  Marin.van.Heel
    email:  marin.vanheel(A_T)gmail.com 
            marin.vanheel(A_T)lnnano.cnpem.br 
    and:    mvh.office(A_T)gmail.com 

--
    Emeritus Professor of Cryo-EM Data Processing
    Leiden University
--
    Emeritus Professor of Structural Biology
    Imperial College London
    Faculty of Natural Sciences
    email: m.vanheel(A_T)imperial.ac.uk 
--

I receive many emails per day and, although I try,
there is no guarantee that I will actually read each incoming email.





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Re: [ccp4bb] Help with omit map

[Eugene Osipov]

Vikram,
you can use phenix.polder program.

2018-07-24 22:26 GMT+03:00 Vikram Dalal :

> Hi everyone,
>
>
> I have to generate the omit map of metal and coordinating residues of
> protein structure for the figure.
>
> Which program can be used to generate the omit map for my requirement.
>
>
>
> Thanks & Regards,
>
>
>
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



-- 
Eugene Osipov
Junior Research Scientist
Laboratory of Enzyme Engineering
Research Center of Biotechnology
Russian Academy of Sciences
Leninsky pr. 33, 119071 Moscow, Russia
e-mail: e.m.osi...@gmail.com



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[ccp4bb] Help with omit map

[Vikram Dalal]

Hi everyone,


I have to generate the omit map of metal and coordinating residues of
protein structure for the figure.

Which program can be used to generate the omit map for my requirement.



Thanks & Regards,



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[ccp4bb] ESRF workshop on sample preparation for Cryo-EM

[David FLOT]

(on behalf of the organisers)

Dear All,

We are pleased to announce a 2 day practical workshop on sample
preparation for cryo-EM single particle data collection jointly
organised by the ESRF, EMBL Grenoble and the IBS. This is the first of a
series of practical hand-on workshops to come in the future. This
workshop is aimed at PhDs, Postdocs and young scientists new to the
field of single particle cryo-EM and will be held at the European
Synchrotron in Grenoble, France from September 18th to 19th 2018. During
the course, participants will learn theoretical and practical aspects of
sample preparation for single particle cryo-EM.

There is no registration fee and meals and accommodation during the
workshop will be provided free of charge. However, participants should
arrange and pay for their own travel to/from Grenoble. A maximum of 12
participants will be selected and we will accept a limited number of
participants’ samples to be tested during the workshop. In the case
that you plan to bring your own sample(s), please clearly mention this
in your cover letter, also indicating the importance of the project.
Application for the workshop should be supported by a motivation letter
and a CV. Registration is open and can be done using the link
http://www.esrf.fr/home/events/conferences/area-events/esrf-events-list/cryo-em-workshop.html. 


The deadline for application is August 31st. Successful candidates will
be informed during the first week of September.

Best regards,
Workshop organisers

--

 
Dr David FLOT

Beam-Line Operation Manager Tel : (+33) 4 76 88 17 63
Structural Biology GroupFax : (+33) 4 76 88 26 24
ESRF
e-mail : david.f...@esrf.fr http://www.esrf.eu
Room: 30.1.13

Physical addressPostal address
ESRF-The European Synchrotron   ESRF-The European Synchrotron
71, Avenue des Martyrs  CS40220
Grenoble, France38043 Grenoble Cedex 9
France



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[ccp4bb] EChemInfo workshop Oxford: September 3rd-7th

[rachael.sky...@diamond.ac.uk]

Dear All:
After the successful Milano workshop last week, we are now entering the hot 
phase of preparing for the next Training and Innovation Course in Drug Design 
taking place
Mon, 03. Sep. 2018 - 09:00 to Fri, 07. Sep. 2018 - 15:00
at Diamond House, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 
0DE, UK8
Besides the high-quality scientific lectures, tutorials and the time for 
intense scientific discussions accelerating the participants' research 
projects, the highlights of the workshop will be a tour through the Diamond 
light source and punting in Oxford.
For further information, please visit 
http://www.echeminfo.com/events/echeminfo-oxford-2018 
 or contact us.
Bursary Awards are available (deadline 01. August) at 
http://www.echeminfo.com/bursary-awards
Early-bird reduced rates are still available until 01. August.
About eChemInfo: This series of workshops provides a set of stimulating 
lectures and group work sessions using state-of-the-art and emerging modelling 
techniques of relevance to chemists, life scientists and modellers working in 
rational drug design. Participants return to their labs with new ideas, best 
practices and software experiences to maximise productivity in their own drug 
discovery research activities.
Main topics covered are: virtual screening, ligand-based and structure-based 
drug design, bio- and cheminformatics, molecular dynamics simulation, drug 
delivery modelling, systems biology and biotech drug design. The 
functionalities of tools developed in academic groups and from the main 
software providers will be explored based on tutorials and more important on 
case studies taken from ongoing research.

Use the “bring your own problems” option to directly apply your newly acquired 
knowledge to your own research, profit from specific advice by the experts and 
other participants and contribute to innovative approaches for all case studies.


Rachael Skyner
PDRA (XChem)

Diamond Light Source Ltd.
Diamond House, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE

Tel:  +44(0)1235 56 7537
Mobile: +44(0)7540 95 5786 (Out of office)

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please notify us of receipt by returning the e-mail and do not use, copy, 
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[ccp4bb] 1 Day UK-Korea Structural Biology Symposium - 16th August -@DIAMOND LIGHT SOURCE Registration closes TODAY!

[martin.wa...@diamond.ac.uk]

Dear all, don’t miss out on a great day of structural biology at Diamond Light 
Source and a unique opportunity to hear about research and infrastructure in 
South Korea ..today is last day for registration with only a limited number of 
places left – first come first serve on these remaining places!

Full details and registration here:
http://www.diamond.ac.uk/Home/Events/2018/UK-Korean-Structural-Biology-Symposium.html

==
Dear all we are pleased to announce a 1 day structural biology symposium at 
Diamond covering exciting research and topics in MX, CryoEM, XFELs and MicroED 
on the 16th August. The symposium is a unique opportunity for UK structural 
biologists to learn more about structural biology research and infrastructure 
in South Korea as well as get a chance to hear the latest from leaders in these 
areas of structural Biology.

Places are limited and so I urge you all to register quickly to guarantee a 
place! We will also offer some support through a small number of travel 
bursaries for UK based participants to help with costs towards travel for 
students, post-docs and early career scientists to attend the symposium

Full details of the symposium and registration can be found here: 
https://www.diamond.ac.uk/Home/Events/2018/UK-Korean-Structural-Biology-Symposium.html

Thanks
Martin

--
Martin A. Walsh,
Life Sciences Deputy Director &
Group Leader at the Research Complex at Harwell,
Diamond Light Source,
Diamond House,
Harwell Science & Innovation Campus,
Didcot OX11 0DE,
UK
T:+44 1235 778518
E: martin.wa...@diamond.ac.uk


-- 
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




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[ccp4bb] 3-year Postdoc/Assistant Professor Fellowship in GPCR crystallography and cryo-EM

[Jette Sandholm Jensen Kastrup]

To apply the following link needs to be used: 
https://candidate.hr-manager.net/ApplicationForm/SinglePageApplicationForm.aspx?cid=1307=19005=147584=4638
(an email will not be considered)

Deadline: 15 August 2018


The UCPH Receptor Structural Biology Group (Kastrup group) and Computational 
Drug Design Group (Gloriam group), Department of Drug Design and Pharmacology, 
University of Copenhagen wish to employ a joint Post Doc in G protein-coupled 
receptor (GPCR) crystallography. The position starts 1. September 2018 or soon 
thereafter (latest Jan 1st) and lasts for 3 years.

Groups
Professor Jette Sandholm Kastrup, UCPH 
(http://drug.ku.dk/research/biostructural_research/)
 has a strong track record of producing receptor crystal structures (~100 
receptor structures deposited in the Protein Data Bank). She has a strong 
international network with leading medicinal chemists and pharmacologists.

The Gloriam group 
(www.gloriamgroup.org)
 conducts computational drug design, tightly integrated with leading chemists 
and pharmacologists, and structure-function studies of G protein-coupled 
receptors (GPCRs) – one of the largest drug target families. The group has in 
the last two years published in e.g. Nature, Cell, Nature Reviews in Drug 
Discovery, Nature Chemistry and Nucleic Acids Research.

Project
This Post Doc fellowships is one of five that will take part in an ambitious 
interdisciplinary project spanning chemistry, pharmacology, structural biology, 
computational drug design and scientific database development. It is supported 
by the Novo Nordisk Foundation (Hallas-Møller Ascending Investigator) and 
headed by David Gloriam. The project focuses on GPCR biased signalling to 
illuminate the pathways to function and disease.

The overall objective of the project is to establish a joint public platform to 
consolidate the GPCR signalling field, and to identify novel mechanisms and 
ligands of biological and therapeutic relevance. The Post Doc within 
crystallography/cryo-EM will focus on (preferably biased) agonist complexes 
with the Free Fatty Acid 4 (FFA4) receptor, as well as other receptors for 
which structures are known but none with biased agonists. GPCR crystallisation 
requires comprehensive construct engineering to achieve optimal protein 
stability, expression in both insect and mammalian cells, homogeneity and 
crystal packing. The quality of the constructs will be evaluated based on the 
receptor yield and aggregate/monomer ratio (size-exclusion chromatography), as 
well as the thermostability (thermoshift assay). Crystallisation trials will 
benefit from our new state-of-the-art Crystal Gryphon LCP robot capable of 
efficiently screening numerous construct-condition combinations. Cryo-EM 
studies will take advantage of new state-of-the-art core facilities in Denmark.

Qualification requirements  Mandatory requirements

  *   A PhD degree within structural biology
  *   Solid experience with expression and purification of membrane proteins
  *   Demonstrated ability to independently learn new concepts and solve 
biological problems
  *   Excellent communication skills: fluency in English and experience in 
writing scientific texts

Additional meriting qualifications  Experience of, and skills in:

  *   G protein-coupled receptors
  *   Protein crystallography/cryo-EM
  *   Analysis of molecular structures and interactions
  *   Experience with crystallographic software packages

General job description   Your key tasks as a Post Doctorial fellow at the 
Faculty are to:

  *   Manage and carry through your research project
  *   Write scientific articles
  *   Participate in the education and guidance of students

Additional requirements to be hired as an assistant professor
To be hired in the assistant professor the applicant should already have done a 
postdoc, supervised PhD students and have additional qualifications to document 
progression towards a competitive career (high-impact publications, own grants 
etc.). Employment as assistant professor includes teaching obligations and the 
possibility to upgrade pedagogical qualifications.

Key criteria for the assessment of applicants

  *   Professional qualifications relevant to the project
  *   Relevant work experience
  *   Publications
  *   Other professional activities
  *   Language skills
  *   Good interpersonal skills

Terms of employment
The post will be filled according to the Agreement between the Danish Ministry 
of Finance and the Danish Confederation of Professional Associations. The post 
is covered by the Protocol on Job Structure.

Questions
For further information about the post, please contact Professor Jette Sandholm 
Kastrup via j...@sund.ku.dk or David Gloriam via 
david.glor...@sund.ku.dk.

Application
The application,