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<mailto:0000488a26d62010-dmarc-requ...@jiscmail.ac.uk>
Enviado:quinta-feira, 29 de dezembro de 2022 13:20
Para: CCP4BB@JISCMAIL.AC.UK<mailto: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 <bshaa...@bgu.ac.il>
Date: Dec 28, 2022 17:13
Subject: Re: [ccp4bb] Calculate charge on protein surface
To: Rafael Marques <rafael_mmsi...@hotmail.com>
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 <rafael_mmsi...@hotmail.com> 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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