[ccp4bb] [Off-topic] NMR manager position available

[PULSARSTRIAN]

There is a NMR manager position available at University of Oklahoma.

*NMR Manager position at University of Oklahoma  *

*Organization:* Chemistry/Biochemistry

*Job Location:* Oklahoma-Norman-Norman Campus

*Schedule:* Full-time

*Work Schedule:* Monday - Friday 8-5

*Salary Range:* Target Salary $85,000 based on experience

*Benefits Provided:* Yes

*Required Attachments:* Resume, Cover Letter



Job can be applied via following link:

https://ou.taleo.net/careersection/2/jobdetail.ftl?job=222915=GMT-08%3A00=PST8PDT

Regards,

Bhanu



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Re: [ccp4bb] Way to resolve Ramachandra outliers in a structure

[Medhanjali DasGupta]

Very helpful, thank you so much!

Medhanjali

On Fri, Mar 3, 2023, 10:48 AM Nicholas Clark  wrote:

> Hi Medhanjali,
>
> In Coot, there are two additional options for "automated" correction of
> Ramachandran outliers. You can find them under "Calculate".
>
> For the entire structure in the "Calculate->all molecule" tab, select
> Refine/Improve Ramachandran Plot. For a specific region, you can use the
> "Calculate->fit loop->fit loop by rama search". These will attempt to fit
> to the Ramachandran plot but may still revert during subsequent refinement.
> Hope this helps.
>
> Best,
>
> Nick Clark
>
> On Fri, Mar 3, 2023 at 11:24 AM Medhanjali DasGupta <
> medhanjalidasgu...@gmail.com> wrote:
>
>> Hello all!
>>
>> Is there an easy way to fix the backbone angles in a protein structure to
>> fix the Ramachandran outliers in said structure?
>>
>> Coot has the "Edit backbone torsions" option but wondering if there's any
>> other tools available in coot or elsewhere?
>>
>> Thanks
>> Medhanjali Dasgupta
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> 
>>
>
>
> --
> Nicholas D. Clark (He/Him)
> PhD Candidate
> Malkowski Lab
> University at Buffalo
> Department of Structural Biology
> Jacob's School of Medicine & Biomedical Sciences
> 955 Main Street, RM 5130
> Buffalo, NY 14203
>
> Cell: 716-830-1908
>



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Re: [ccp4bb] Way to resolve Ramachandra outliers in a structure

[Nicholas Clark]

Hi Medhanjali,

In Coot, there are two additional options for "automated" correction of
Ramachandran outliers. You can find them under "Calculate".

For the entire structure in the "Calculate->all molecule" tab, select
Refine/Improve Ramachandran Plot. For a specific region, you can use the
"Calculate->fit loop->fit loop by rama search". These will attempt to fit
to the Ramachandran plot but may still revert during subsequent refinement.
Hope this helps.

Best,

Nick Clark

On Fri, Mar 3, 2023 at 11:24 AM Medhanjali DasGupta <
medhanjalidasgu...@gmail.com> wrote:

> Hello all!
>
> Is there an easy way to fix the backbone angles in a protein structure to
> fix the Ramachandran outliers in said structure?
>
> Coot has the "Edit backbone torsions" option but wondering if there's any
> other tools available in coot or elsewhere?
>
> Thanks
> Medhanjali Dasgupta
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
>


-- 
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908



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[ccp4bb] Way to resolve Ramachandra outliers in a structure

[Medhanjali DasGupta]

Hello all!

Is there an easy way to fix the backbone angles in a protein structure to
fix the Ramachandran outliers in said structure?

Coot has the "Edit backbone torsions" option but wondering if there's any
other tools available in coot or elsewhere?

Thanks
Medhanjali Dasgupta



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Re: [ccp4bb] Tools for structure-based multiple sequence alignment

[Pietro Roversi]

Dear Manoj,

I usually utilize SALIGN to produce structure-based sequence alignments:

https://modbase.compbio.ucsf.edu/salign/

Ciao

Pietro

On 02-03-2023 08:45, Manoj N wrote:

Dear all,

We want to generate a structure-based multiple
sequence alignment for a large number of homologous structures (>100).


What are the available programs (stand-alone or webserver) to do this?


Thank you,

Best wishes,

Manoj

-

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--
Dr. Pietro Roversi, PhD
Italian National Research Council (CNR)
Institute of agricultural biology and biotechnology (IBBA-CNR)
Via Edoardo Bassini 15, 20133 Milano, Italy
Tel. +39 02 23699428
Mobile +39 351 6800096
Fax: +39 02 23699411
https://ibba.cnr.it/en/staff/pietro-roversi/

Adjunct Lecturer in Mathematical Modeling for Biology
Master in Quantitative Biology,
Department of Biosciences, University of Milano, Italy
Email: pietro.rove...@unimi.it
URL: https://www.unimi.it/en/ugov/person/pietro-roversi

Honorary Lecturer at LISCB - Department of Molecular and Cell Biology
Leicester University, Lancaster Rd.
Leicester LE1 7HB, England, UK
Tel. +44 7927 952047
Email: pr...@leicester.ac.uk
URL: 
https://le.ac.uk/liscb/research-groups/honorary-members/pietro-roversi




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[ccp4bb] Job opening for a post-doctoral research fellow in the cryo-EM facility of the European Synchrotron, ESRF, France

[David FLOT]

 Forwarded Message 
Subject: 	Job opening for a post-doctoral research fellow in the cryo-EM 
facility of the European Synchrotron, ESRF, France

Date:   Fri, 3 Mar 2023 09:28:36 +0100
From:   Eaazhisai KANDIAH 
Organization:   ESRF
To: cc...@jiscmail.ac.uk



Dear Colleagues,

I'd like to draw your attention to a job opening for a *post-doctoral 
research fellow in the cryo-EM facility of the European Synchrotron, 
ESRF, France*


CM01 is the ESRF’s cryo-EM facility dedicated to performing 
high-resolution imaging of biological macromolecules, particularly for 
the structural analysis of large, difficult to crystallize, 
protein-protein or protein-nucleic acid complexes. CM01 has been 
designed to complement, and create synergy with, the existing ESRF 
macromolecular crystallography and BioSAXS beamlines and it is operated 
as a joint effort from the four institutes (ESRF, EMBL, IBS and ILL) 
located on the EPN campus. CM01 is equipped with a Krios G3 microscope 
and state-of-the-art K3 direct electron detector and a GATAN LS Quantum 
energy filter. CM01 offers single particle analysis (SPA) to users 
worldwide, and in the near future cryo-electron tomography (cryo-ET) as 
well. For more details on CM01, click here .


The postdoctoral position available will focus on the method development 
in areas important for CM01 notably in SPA data analysis and cryo-ET. As 
for all postdoctoral researchers in the Structural Biology Group, the 
successful candidate will contribute to the operation of CM01 and will 
provide support to external users as local contact. Furthermore, the 
selected candidate will also participate in a research program aimed at 
the structural characterization of the non-structural proteins of 
coronavirus and in particular of SARS-CoV2. The research project focuses 
on the molecular mechanisms of three non-structural proteins in viral 
replication by employing an integrative structural biology approach, 
including cryo-ET and SPA.


For direct inquiries, please contact Eaazhisai Kandiah 
(eaazhisai.kand...@esrf.fr).


*Expected profile*

 * PhD in biophysics, biology or closely related science obtained less
   than 3 years ago
 * A strong background in cryo-EM
 * A strong interest in method development for cryo-EM
 * Background in structural biology and protein production is desirable
 * Knowledge of membrane proteins is an asset
 * Ability to interact with multi-disciplinary staff and facility users
 * Proficiency in English (working language at the ESRF)

More information on the working conditions and the *application portal* 
are found here .


Kindly please forward this email to relevant colleagues who might be 
interested. Thanks very much!


Best wishes

Isai

--

*Dr. Eaazhisai Kandiah*

CM01 beamline

https://www.esrf.fr/CM01

71 Avenue des Martyrs, 38000 Grenoble
Telephone: +33 476 882691
Email: eaazhisai.kand...@esrf.fr 



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