an apology, don't attach the file correctly, here it goes, regards ATTE Fernando Villa Díaz El lun., 16 de sep. de 2019 a la(s) 15:20, Fernando Villa ( fer.vdl1928@gmail.com) escribió:
Dear Tom and Chimera users,
In ChimeraX or Chimera, is it possible to calculate the number of vertices and their respective total charges?
I calculated the electrostatic potential surface (Coulombic) with another program, it gave me the following results (attached in this email) and I calculated the area in red and blue, above and below a threshold = 0.
Unfortunately, these results do not help me, because I need to obtain an electrostatics calculations from Adaptive Poisson-Boltzmann Solver (Calculations that I have already made for study proteins with PDB2PQR and APBS, in interface with Chimera: .pqr and .dx files and emulated in Chimera X)
e.g. [image: image.png]
Now my question is: Can I obtain these results of vertices and charges in a file from Chimera or Chimera X (possibly .cvs, .txt, etc.), so that I can make the corresponding calculations?
I would greatly appreciate your help
best regards,
Fer
El lun., 16 de sep. de 2019 a la(s) 13:03, Tom Goddard (goddard@sonic.net) escribió:
Hi Fernando,
Instead of thinking about the coloring, it would be clearer to ask how much surface area has electrostatic potential value >= 5. Chimera does not have any code to compute that, although it is something we could add to ChimeraX.
Tom
On Sep 11, 2019, at 7:27 PM, Fernando Villa <fer.vdl1928@gmail.com> wrote:
Dear all Chimera users
In UCSF ChimeraX version 0.91 (2019-08-30) I opened a .pqr file (generated with pdb2pqr in Chimera 1.14) and then I opened a .dx file (generated with APBS in Chimera 1.14)
Then I input the commands:
surface color electrostatic #1 map #2 palette -10,red:0,white:10,blue
<image.png> Is it possible to calculate the red and blue area in Å2 of the molecule?
Best regards,
Fernando
ATTE Fernando Villa Díaz
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
