Re: [Chimera-users] Interpreting field / force direction in Coulombic Surface Coloring
Hi Sumitro, The interaction energy of a "test" charge at some point would be the charge multiplied by the electrostatic potential. So if the test charge is -1 e (like one electron) its interaction energy at a point with potential +10 kcal/(mol.e) would be favorable, -10 kcal/mol. Positive potential favors interaction with negative charges and vice versa. I hope this clarifies, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco P.S. better to send questions to chimera-users@cgl.ucsf.edu because if you send to me and I'm on vacation, you might not get answered On May 18, 2012, at 12:36 AM, Sumitro Harjanto wrote:
Hi Elaine, I have a simple question regarding the Coulombic Surface Coloring. I understand that the potential are generated by assuming a charged probe that moves along the surface of the model and as it traverses the surface the potential is picked up as the calculated electrostatic force the probe should experience (that's my understanding, correct me if I'm wrong please).
I am just, however, a little confused about the interpretation of the value. say if I got a blue patch on the surface, which means I'm getting values in the range of ~10 (positive) kcal/(mol·e) at 298 K; does that mean the region indicated by the blue patch should potential attract or repel electron? Thanks! Cheers, Sumitro
Hi elaine, so does blue patch (positive interaction energy) mean positively charged or negatively charged surface? On May 19, 2012 1:16 AM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Hi Sumitro, The interaction energy of a "test" charge at some point would be the charge multiplied by the electrostatic potential. So if the test charge is -1 e (like one electron) its interaction energy at a point with potential +10 kcal/(mol.e) would be favorable, -10 kcal/mol. Positive potential favors interaction with negative charges and vice versa. I hope this clarifies, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
P.S. better to send questions to chimera-users@cgl.ucsf.edu because if you send to me and I'm on vacation, you might not get answered
On May 18, 2012, at 12:36 AM, Sumitro Harjanto wrote:
Hi Elaine, I have a simple question regarding the Coulombic Surface Coloring. I understand that the potential are generated by assuming a charged probe that moves along the surface of the model and as it traverses the surface the potential is picked up as the calculated electrostatic force the probe should experience (that's my understanding, correct me if I'm wrong please).
I am just, however, a little confused about the interpretation of the value. say if I got a blue patch on the surface, which means I'm getting values in the range of ~10 (positive) kcal/(mol·e) at 298 K; does that mean the region indicated by the blue patch should potential attract or repel electron? Thanks! Cheers, Sumitro
The color shows the value of the potential. If you are using default coloring settings, blue is for positive potential, red for negative potential. Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 20, 2012, at 4:39 AM, Sumitro Harjanto wrote:
Hi elaine, so does blue patch (positive interaction energy) mean positively charged or negatively charged surface?
Hi elaine, so can I say that blue surface (positive potential) is positively charged and has the tendency to attract negative charges? On May 22, 2012 1:48 AM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
The color shows the value of the potential. If you are using default coloring settings, blue is for positive potential, red for negative potential. Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 20, 2012, at 4:39 AM, Sumitro Harjanto wrote:
Hi elaine, so does blue patch (positive interaction energy) mean positively charged or negatively charged surface?
Hi Sumitro, Yes, positive potential favors interaction with negative charges and vice versa. <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-May/007591.html> For example, in this tutorial, Coulombic coloring shows a blue (positive potential) pocket binding a highly negatively charged ligand. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html#esp> Elaine On May 21, 2012, at 5:12 PM, Sumitro Harjanto wrote:
Hi elaine, so can I say that blue surface (positive potential) is positively charged and has the tendency to attract negative charges?
On May 22, 2012 1:48 AM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote: The color shows the value of the potential. If you are using default coloring settings, blue is for positive potential, red for negative potential. Elaine
On May 20, 2012, at 4:39 AM, Sumitro Harjanto wrote:
Hi elaine, so does blue patch (positive interaction energy) mean positively charged or negatively charged surface?
Dear all, I'm using Chimera 1.6.1 on Ubuntu 11.04 and it seems addH doesn't work for DNA. I either select the chain or tried without select and in both cases no hydrogens were added to the chain. It's a bug? Thanks, Maroo Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 www.rete29aprile.it ---------------------------------------------------------------- Invito da parte dell'Ateneo: Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata codice fiscale: 80213750583 http://5x1000.uniroma2.it
Hi, problem solved. It seems to be an unexpected geometry for the first nucleotide. Sorry, Marco sette@uniroma2.it ha scritto:
Dear all,
I'm using Chimera 1.6.1 on Ubuntu 11.04 and it seems addH doesn't work for DNA. I either select the chain or tried without select and in both cases no hydrogens were added to the chain. It's a bug? Thanks, Maroo
Dr.Marco Sette, Ph.D.
Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328
www.rete29aprile.it
---------------------------------------------------------------- Invito da parte dell'Ateneo: Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata codice fiscale: 80213750583 http://5x1000.uniroma2.it
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 www.rete29aprile.it ---------------------------------------------------------------- Invito da parte dell'Ateneo: Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata codice fiscale: 80213750583 http://5x1000.uniroma2.it
participants (3)
-
Elaine Meng -
sette＠uniroma2.it -
Sumitro Harjanto