Re: [ccp4bb] Coot RNA bases Mutate

2022-08-08 Thread Paul Emsley 

On 06/08/2022 09:08, Cryo EM wrote:

Hi everyone,

I am trying to mutate modified RNA nucleotide to standard nucleotide 
by coot using "Simple Mutate" button. But it is not working despite 
selecting the correct residue from the standard base list that pop up 
on clicking "simple mutate button". Does anyone and an idea what 
could be the problem? Or is this wrong way to do that?


I am using coot 0.9.8.3 EL (Ccp4) on my Mac.



What does it say in the terminal? - that should give you a clue. My 
guess is that coot can't auto-superpose onto a non-standard nucleotide.


Try "Replace Residue" instead.

Paul



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Re: [ccp4bb] Missing restrains for standard amino acid

2022-08-08 Thread Paul Emsley 

On 07/08/2022 07:00, Cryo EM wrote:

Hi everyone,

I am using Coot 0.9.8.3 EL (ccp4) on my iMac M1 with MacOS Monterey. 
The phenix version I am using is 1.20.1-4487.


At the end of validation run or real space refinement for my cryo-EM 
map, I want to fix the problems in the model interactively by the 
"open in coot" button displayed in phenix. As soon as I click on the 
problems list in phenix, coot takes me to that atom but I am not able 
to do any local real space refinement in coot since it complains about 
the missing restrains for even standard amino acids and nucleotides 
(screenshot attached).


Please note that coot alone (when not connected to phenix) works for 
me flawlessly. I guess it has something to do with the missing monomer 
library path in coot when connected to phenix but I am unable to fix 
this. Can someone please redirect me to the solution?



Sounds like the monomer library installation is borked.

What does it say in the terminal?

Paul.



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[ccp4bb] Joint Instruct-iNEXT Course - September 25-30 - Oeiras (Portugal)

2022-08-08 Thread Jose Artur Brito 

(message sent on behalf of Dr. Margarida Archer)


Dear colleagues,

A Joint Instruct-iNEXT Course on Integrative Structural Biology (incl. 
X-ray Crystallography, Nuclear Magnetic Resonance, Magnetic Resonance 
Mass Spectrometry and Electron Microscopy) will take place in September 
25-30, nearby Lisbon, Portugal. The main goal is to provide the basic 
concepts and hands-on applications of MX, NMR, MRMS and single-particle 
analysis cryo-EM. Their  strengths, limitations and complementarity will 
be discussed to achieve integrative structural biology approaches to 
tackle challenging projects. The participants will become acquainted 
with the technology catalogues provided by Instruct-ERIC and 
iNEXT-Discovery and will need to select a case study and prepare an 
access proposal to use these platforms. The course is aimed primarily at 
PhD and early post-doc students and will be limited to 20.


As we still have a few places available, the registration deadline has 
extended to August 19. More details can be found at 
https://louro98.wixsite.com/website2022.



We´re looking forward to welcoming you in Lisbon!

The Organising Committee,
Margarida Archer (ITQB NOVA), Carlos Cordeiro (FC-UL) and Ricardo Louro 
(ITQB NOVA)



--

*  Jose Artur Brito, PhD   *
*  *
*  Membrane Protein Crystallography Laboratory *
*  Instituto de Tecnologia Quimica e Biologica Antonio Xavier  *
*  Oeiras - PORTUGAL   *
*  *
*  Phone - +351 214 469 760 (office) /  +351 962 452 179 (mobile)  *
*  *
*  Website - http://www.itqb.unl.pt/researchers/jbrito *




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[ccp4bb] 2-year post-doc in membrane protein structural biology available at Lund University

2022-08-08 Thread Pontus Gourdon 
Dear all,

We have an open post-doc position in membrane protein structural biology at 
Lund University, Sweden. Full details are available below.

The closing date for applications is the 31st August.

Do not hesitate to contact us if you have questions regarding the position.

Best regards,

Pontus


Pontus Gourdon, M.Sc., Ph.D., Wallenberg Academy Prolongation Fellow, Lundbeck 
Foundation Ascending Investigator
*
Senior lecturer (lektor) | Dept. of Experimental Medical Science | Lund 
University
Sölvegatan 19 | Office C1320b | SE - 221 84 Lund | Sweden

Associate Professor (lektor) | Dept. of Biomedical Sciences | University of 
Copenhagen
Mærsk Building, Nørre Allé 14 | Office 07-9-75 | DK - 2200 Copenhagen | Denmark

Tel.: +46 739 959856 and +45 5033 9990
Email: pontus.gour...@med.lu.se and pon...@sund.ku.dk
Google scholar:  
rb.gy/tdar1i
Web-LU:  
rb.gy/y2nkpp
Web-KU: 

 rb.gy/bshuqp
*




Work profile
The successful applicant will perform experimental research to understand how 
membrane proteins belonging to the TRP-channel family are regulated in normal 
and pathophysiology using single particle cryo-EM. You should be creative, with 
good interpersonal and collaborative skills, power of initiative, and a high 
degree of independence. In particular, you must master cloning, production, 
purification and analysis of membrane proteins as well as sample preparation, 
data collection, processing and analysis for determination of cryo-EM 
structures. In addition, experience of composing and writing manuscripts is 
considered of importance.

Research environment
The research will be supervised by Prof. Peter Zygmunt in collaboration with 
Assoc. Prof. Pontus Gourdon, together providing the necessary academic 
knowledge and laboratory equipment facilities as well as national and 
international academic networks to successfully investigate the 
structure-function relationship of TRP channels, and in particular the 
requirements for ligand gating mechanisms of TRP channels involved in various 
cellular processes. Prof. Peter Zygmunt has over a time period close to 25 
years established an internationally recognized translational research 
environment at Lund University, focusing on both clinical and molecular aspects 
of TRP channel regulation with prime interest in pain signaling and secretory 
cell signaling. Assoc. Prof. Pontus Gourdon offers know-how in membrane protein 
structural biology. The group of Assoc. Prof. Gourdon is located to Lund 
University as well as to University of Copenhagen.

Selected recent publications from the two groups:

  *   Li et al. (2022) Structures of Atm1 provide insight into [2Fe-2S] cluster 
export from mitochondria. Nature Communications 13(1):4339
  *   Wiuf et al. (2022) The two-domain elevator-type mechanism of 
zinc-transporting ZIP proteins. Science Advances 8, eabn4331
  *   Moparthi et al. (2021). The human TRPA1 intrinsic cold and heat 
sensitivity involves separate channel structures beyond the N-ARD domain. 
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.31.454589; 2021
  *   Grønberg et al. (2021). Structure and ion-release mechanism of PIB-4-type 
ATPases. Elife 10:e73124.
  *   Li et al. (2021). Structure and transport mechanism of P5B-ATPases. 
Nature Communications 25(12):3973
  *   Wang et al. (2021). Cryo-EM reveals the architecture of placental malaria 
VAR2CSA and provides molecular insight into chondroitin sulfate binding. Nature 
Communications 12:2956.
  *   Moparthi and Zygmunt PM (2020). Human TRPA1 is an inherently 
mechanosensitive bilayer-gated ion channel. Cell Calcium. 91:102255.


Scholarship period: The scholarship covers a period of maximum 24 months.



Application deadline: August 31st, 2022



Preliminary start date: October 1st, 2022, or according to agreement



Supervisor/contact person:

Peter Zygmunt, +46 (0)46-222 69 06, peter.zygm...@med.lu.se

Pontus Gourdon, +46 (0)739-95 98 56, pontus.gour...@med.lu.se



Qualifications:

  *   To be eligible for a post-doc scholarship at Lund University the 
recipient must hold a PhD degree within a relevant field. The PhD degree must 
not be from Lund University. The PhD degree must not be older than three years, 
unless special reasons may be invoked such as: illness, parental leave, 
commission of trust, military/civil defense service or similar missions. The 
applicant must not have been employed at Lund University in the past two years.
  *   PhD in structural biology, protein chemistry or equivalent research 
area

[ccp4bb] Postdoc Opportunity - Multidataset X-ray Crystallography, Computational Structural Biology, & Protein Allostery - Upper Manhattan, New York City

2022-08-08 Thread Keedy, Daniel 
Hello ccp4bb community,

The Keedy Lab at the CUNY Advanced Science Research Center in New York City has 
a funded Postdoctoral Scholar position available immediately.  We seek 
applications from individuals with experience in computational biology, 
computer science, software development, biochemistry, biophysics, or a related 
area.  Details of research projects and career training will be tailored to the 
goals of the successful applicant.

Research:  The Keedy Lab is interested in the interplay between protein 
sequence, conformational heterogeneity, and biological function.  Using a 
unique combination of avant-garde computational and biophysical approaches, we 
aim to elucidate the conformational ensembles of proteins and to understand how 
they are shifted by perturbations, including temperature, pressure, mutations, 
ligands, protein:protein interactions, to control biological function.  The 
successful applicant for this open position will join these efforts by 
developing and using new computational approaches to exploit families of 
related structures, extract hidden signatures of conformational heterogeneity, 
and explore how changes to amino acid sequence rewire protein allosteric 
networks.

Location:  The CUNY Advanced Science Research Center (https://asrc.gc.cuny.edu) 
is a cutting-edge research institution, perched atop a hill overlooking Harlem 
in New York City.  Alongside its sister research building, the City College of 
New York’s Center for Discovery and Innovation, the ASRC sits in an oasis of 
green amidst upper Manhattan.  The ASRC Structural Biology Initiative 
(https://asrc.gc.cuny.edu/structbio) features eight tenure-track and 
research-track faculty members, pursuing diverse research problems using X-ray 
diffraction, mass spectrometry, cryo-EM, NMR, solution biophysics, and advanced 
microscopy.  The ASRC is immediately adjacent to the New York Structural 
Biology Center, a consortium of CUNY and eight other New York academic 
institutions with world-class facilities, and is just 70 miles from Brookhaven 
National Laboratory, featuring the National Synchrotron Light Source II – the 
brightest synchrotron light source in the United States.

You can read more about the Keedy lab here:
https://keedylab.org

Please officially apply for the position here:
https://www.rfcuny.org/careers/postings?pvnID=RC-2207-004956

You may also email me directly to ask questions or discuss.

I look forward to hearing from you!

Best regards,

Daniel Keedy

—
Daniel A. Keedy, PhD
Assistant Professor
Structural Biology Initiative, CUNY Advanced Science Research Center
Department of Chemistry and Biochemistry, City College of New York
Biochemistry, Biology, and Chemistry PhD Programs, CUNY Graduate Center
dke...@gc.cuny.edu  |  https://keedylab.org   |  
919-724-6064




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[ccp4bb] Making bonds

2022-08-08 Thread Cryo EM 
Hi everyone,

In one my PDBs, I see that there is a linkage break in ribonucleotides.
Specifically one of the phospodiester bond seems to be broken and thus O3'
needs to be bonded to P atom of next nucleotide. What is the easiest way to
do this in coot ? Or any other software?
I tried "make link" option in coot but it seems it just created link in PDB
and not bond?


Regards



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[ccp4bb] Post Doc job opening

2022-08-08 Thread Wei Zhang 
Dr. Wei Zhang's lab at University of Minnesota, USA, is seeking a
structural biologist to study membrane fusion driven by viral envelope
proteins. For details about the position, please visit
https://hr.myu.umn.edu/jobs/ext/350586

Job ID: 350586



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