Re: [ccp4bb] Coot on MacOS Ventura

[Paul Emsley]

Hello Elsa,

On 30/12/2022 17:13, Elsa Garcin wrote:

Is it possible to run coot on MacOS Ventura and xquartz version 2.8.4?
I believe so, but people have reported minimizing window when they try 
to do so.

I tried installing coot with homebrew (instructions from Scottlab webpage),


This is a quite different beast.


  but was not successful.
I have been trying to work out what has gone wrong and how to fix it. 
Still trying.

Has anyone figured out how to install it so it runs properly? If so, could you 
please share how you did it?


Mac OSX is not my most frequently-used platoform. I will keep bashing 
away at it.


The situation is under discussion in issue 33 on the github page.

Paul.



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[ccp4bb] Coot on MacOS Ventura

[Elsa Garcin]

Hello all,
Is it possible to run coot on MacOS Ventura and xquartz version 2.8.4?
I tried installing coot with homebrew (instructions from Scottlab webpage), but 
was not successful.
Has anyone figured out how to install it so it runs properly? If so, could you 
please share how you did it?
Thank you.
Cheers
E.



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[ccp4bb] RES: [ccp4bb] Fwd: Re: [ccp4bb] Calculate charge on protein surface

[Rafael Marques]

Thank you very much, guys. What I wanted actually was a software that gives the 
formal charge looking at different axis of my model instead of particular 
residues. Then, placing the center of my model at coordinates 0,0,0, I would be 
able to see the sum up of charges at +/- x, +/-y and +/-z. I will take a look 
on the sites and in chimera.

Best wishes


Rafael Marques da Silva
PhD Student – Structural Biology
University of Leicester

Mestre em Física Biomolecular
Universidade de São Paulo

Bacharel em Ciências Biológicas
Universidade Federal de São Carlos

phone: +55 16 99766-0021

   "A sorte acompanha uma mente bem treinada"


De: Jon Cooper
Enviado:quinta-feira, 29 de dezembro de 2022 13:20
Para: CCP4BB@JISCMAIL.AC.UK
Assunto: Re: [ccp4bb] Fwd: Re: [ccp4bb] Calculate charge on protein surface

Dear Boaz

I think your original answer must have been steganographic ;-0 Maybe white text 
on a white background ;-? Anyway, I can see it below now that I have started 
typing this reply, and advice is excellent.

My answer to Rafael's question would be to look at apbs:

https://www.poissonboltzmann.org/

This gives you a map of the potential. It's a while since I dabbled with it, 
but I remember using it and it was all pretty workable as a standalone program, 
even for an electrostatics non-specialist. You might need to do some scripting 
to sum up charges, etc, though.

Good luck. Jon.C.

Sent from ProtonMail mobile



 Original Message 
On 28 Dec 2022, 15:57, Boaz Shaanan < bshaa...@bgu.ac.il> wrote:


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben Gurion University
Beer Sheva, Israel
-- Forwarded message --
From: בעז שאנן 
Date: Dec 28, 2022 17:13
Subject: Re: [ccp4bb] Calculate charge on protein surface
To: Rafael Marques 
Cc:

Hi
In ucsf-chimera you can "walk" with the cursor on the surface and it'll show 
the actual porential value at each point in the command line. You have to 
enable this option in the surface drawing panel. I've used this option quite 
often. There may be a similar option in chimerax by now.
My 2p.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben Gurion University
Beer Sheva, Israel

On Dec 28, 2022 17:03, Rafael Marques  wrote:

Hello guys. I hope you are having a great break and still eating the leftovers 
of your Xmas turkey.



I wonder if there is any software that could provide me numbers regarding the 
formal charge of different sides of my structure. Although I can clearly see 
that one face of it is pretty red, I would like to know “how much” red it is.



Best wishes



Rafael Marques da Silva

PhD Student – Structural Biology

University of Leicester



Mestre em Física Biomolecular

Universidade de São Paulo



Bacharel em Ciências Biológicas

Universidade Federal de São Carlos



phone: +55 16 99766-0021



   "A sorte acompanha uma mente bem treinada"







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[ccp4bb] Position opening in UC Davis

[Eugene Krissinel - STFC UKRI]

On behalf of Dr. Nitzan Shabek, please see below  -- Eugene Krissinel




Subject: Open postdoctoral position at University of California Davis



The Shabek lab is looking for a postdoctoral fellow with a strong background in 
structural biology to join immediately to our research group at the University 
of California, Davis (shabek-lab.ucdavis.edu/).

We use structure- function approaches to study unique signaling pathways and 
their regulation by the Ubiquitin Proteasome System. We have new funded 
projects by NSF and DOE.



Qualifications:



• Must be a recent Ph.D. in Biochemistry and/or Plant Biology and/or Structural 
Biology

• Experience in molecular biology, protein purification techniques (experience 
with baculovirus expression is preferred but not required), and 
protein-protein/molecule interactions.

• Experience in structural biology (X-ray crystallography and/or Cryo-EM).

• Strong communications skills and ability to train junior scientists



Compensation and benefits for postdocs in UC Davis are the highest in the 
country. Davis is a beautiful Californian town located near Sacramento, and 
close to San Francisco, and several National Parks. The Shabek lab has access 
to ALS beamlines in Berkeley National Labs and SSRL in Stanford, as well as 
CryoEM facilities (BioEM in Davis or Brookhaven National labs).



To apply:



Email directly to Dr. Nitzan Shabek (nsha...@ucdavis.edu) with the subject line:

Postdoc in Structural Biology Application.



Please include a cover letter that highlights your research experience & 
interests, CV, and contact information of 2-3 references.

(please use your institutional email, if possible, otherwise it may go to spam)





__

Nitzan Shabek, Ph.D.

Plant Biology Department

College of Biological Sciences

University of California, Davis

Office: (530)-752-8187

Lab: (530)-754-1580

Email: nsha...@ucdavis.edu

Lab website: https://shabek-lab.ucdavis.edu/




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