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 wrote: > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben Gurion University > Beer Sheva, Israel > ---------- Forwarded message ---------- > From: בעז שאנן <[email protected]> > Date: Dec 28, 2022 17:13 > Subject: Re: [ccp4bb] Calculate charge on protein surface > To: Rafael Marques <[email protected]> > 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 <[email protected]> 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" >> >> ________________________________________________ >> >> --------------------------------------------------------------- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > --------------------------------------------------------------- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
