Hi all Chimera users, I would like to know how to calculate the values of Coulombic ESP on the interface between two proteins: At the moment I have done the following: *UCSF Chimera version 1.14 Commands: open <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/open.html> 1avx display ~longbond <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/longbond.html> split <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/split.html> delete <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html> solvent surf #0.1 Tools>Surface/Binding analysis>Coulombic surface coloring
Check the box compute grid
Apply
Surface color>Options
>Check the box Report value at mouse position >Click color: All the electrostatic potential values appear by Coulombic Kcal/(Mol.e) at the mouse position: [image: imagen.png] Commands: ~surface #0.1 measure buriedArea #0.1 #0.2 select #0.1@/buriedSASArea> 1 surf sel Volume viewer>Tools>Values at atom position>Click Histogram [image: imagen.png] Is there a way to save all the ESP Coulombic values in the selected interface surface in a file? Is it possible to calculate the polar and non-polar surface area in the interface? Regards, Fer. El lun., 16 de sep. de 2019 a la(s) 17:39, Tom Goddard (goddard@sonic.net) escribió:
Hi Fernando,
I don't understand what you need vertex coordinates for. But you could put a print statement into the Chimera Python code that does surface coloring to output vertex coordinates and potential values. This would be in file
chimera/share/SurfaceColor/__init__.py
or on Mac in
Chimera.app/Contents/Resources/share/SurfaceColor/__init__.py
in the volume_values() routine change
def volume_values(self, surface_piece):
p = surface_piece xf = p.model.openState.xform v = p.geometry[0] n = p.normals return self.offset_values(v, n, xf)
to
def volume_values(self, surface_piece):
p = surface_piece xf = p.model.openState.xform v = p.geometry[0] n = p.normals values, outside = self.offset_values(v, n, xf) print '\n'.join('%.5g %.5g %.5g %.5g' % (x, y, z, val) for (x,y,z), val in zip(v, values)) return values, outside
Use the Surface Color tool and the vertices and values will be printed to the reply log.
Tom
On Sep 16, 2019, at 1:20 PM, Fernando Villa <fer.vdl1928@gmail.com> wrote:
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.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
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