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: image.png] Is it possible to calculate the red and blue area in Å2 of the molecule? Best regards, Fernando ATTE Fernando Villa Díaz
Hi Fernando, An important thing to understand is that the color is changed gradually from red to white, and gradually from white to blue. So there is a lot of surface coloring that is “between” red and white, and between white and blue. Only the surface points with values -10 or lower are actually red, and those with 10 or higher are actually blue. It is unclear exactly what quantity you want to measure. There is no simple feature like a command to do it. You would have to use python scripting, but somebody else would have to advise on any details of that. Also, first think carefully about what you really want to measure. This electrostatic surface coloring is really meant for visualization, comparison “by eye.” For quantitative analyses, maybe the two websites I mentioned earlier would be better tools. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
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
Thank you very much Dr. Elaine and the Chimera work group, now I have a better picture of what I have to do. Thank you for guiding me in this part, I appreciate it Best regards, Fer ATTE Fernando Villa Díaz El jue., 12 de sep. de 2019 a la(s) 10:02, Elaine Meng (meng@cgl.ucsf.edu) escribió:
Hi Fernando, An important thing to understand is that the color is changed gradually from red to white, and gradually from white to blue. So there is a lot of surface coloring that is “between” red and white, and between white and blue. Only the surface points with values -10 or lower are actually red, and those with 10 or higher are actually blue. It is unclear exactly what quantity you want to measure.
There is no simple feature like a command to do it. You would have to use python scripting, but somebody else would have to advise on any details of that. Also, first think carefully about what you really want to measure.
This electrostatic surface coloring is really meant for visualization, comparison “by eye.” For quantitative analyses, maybe the two websites I mentioned earlier would be better tools. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
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
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
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
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
Hi Fernando, This is not answering your specific request, but some points that may be important to consider: (1) Electrostatic potential (the values in dx files) is not the same as charge. Maybe you already know that, but I’m just making sure it is clear. The charge on each atom is already in the pqr file, so if you just wanted the total charge of the molecule, you would add those up. You could even select the surface atoms only, and then add their charges. (2) maybe it is not meaningful to count points that have electrostatic potential values very close to zero. (3) similarly, maybe it is not meaningful to consider points with very small values as having equal importance as points with very large values (that is what you are doing if you only care about the sign) (4) the spatial distribution of the values is important for molecular recognition, not just the number of points with some value. It is very different to have positive and negative intermixed all over the molecule, as compared to positive concentrated on one end of the molecule and negative concentrated on the other end, but those two situations might give identical % areas in your calculation. I understand what you want, but I’m concerned it may not be biologically/physically meaningful. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
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 <mailto: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 <mailto: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 <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
<Test_MEP_Protein.xlsx>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
<Test_MEP_Protein.xlsx>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Fernando, You already calculated the values of Coulombic ESP on the interface: it is displayed. However, I guess you mean that you want to write the values that you have already shown with coloring to some file. There is a “surfval.py” python script in the Chimera scripts page that is supposed to do that, although it may be the whole surface (not just the interface), see: <http://www.cgl.ucsf.edu/trac/chimera/wiki/Scripts> The Coulombic Surface Coloring tool (and command) also has an option to open the grid of Coulombic ESP values as as separate model. This grid is what is interpolated to get the values for surface coloring. This separate grid model can be saved using the Volume Viewer tool’s File menu. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html#volume> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html> Getting polar/nonpolar surface area is the same question you asked in September. Here were the responses: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016139.html> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016159.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 30, 2019, at 9:35 AM, Fernando Villa <fer.vdl1928@gmail.com> wrote:
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 1avx display ~longbond split delete 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:
<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
<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
Dear Elaine. Thank you very much, I really appreciate it. I am confused with some data. A few months ago Tom Goddard sent me a phyton code to get the vertex coordinates and the values in Reply log: In Windows: 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 To obtain the output vertex coordinates and potential values: Commands: open 1avx display ~ longbond split delete solvent surf # 0.1 Tools> Surface/Binding analysis>Coulombic surface coloring > Check the box compute grid > Apply
Surface color>Click color = All values Appear in reply log (attached file: 001_xyz-val_ESP.txt) [image: imagen.png] I suppose that the first three numbers are the vertex coordinates and the last value is the ESP Coulombic (Kcal / mol.e).
Value at mouse position:
Surface color> Options > Check the box Report value at mouse position > Click color: [image: imagen.png] All the electrostatic potential values appear by Coulombic [Kcal / (mol.e)] at the mouse position, I suppose they are the same values shown in replylog = file 001_xyz-val_ENG.txt.
However, when I open the surfval.py script Command: surfvalues # 0.1 # 1 ~/Desktop /002_xyz-val_script-val_ENG.txt A file is saved (attached file: 002_xyz-val_script-val_ESP.txt) with the same vertex coordinates. The ESP values in Kcal/(mol.e) are different from 001_xyz-val_ESP.txt. [image: imagen.png] Besides, if I save the values from Volume viewer: Volume viewer> Tools> Values at atom position
Click Histogram> Render / Select by attribute File> Save attribute> Click box “Restrict save to current selection, if any”> File name: 003_@val_ENG.txt> Save (attached file: 003_@val_ENG.txt) The ESP values --> Kcal/(mol.e)
My question is: The files 001_xyz-val_ESP.txt, 002_xyz-val_script-val_ENP.txt, 003_@val_ESP.txt, and the values at mouse position have units in Kcal/(mol.e)? If I'm wrong, let me know please. Regards. Fer. El lun., 30 de dic. de 2019 a la(s) 11:56, Elaine Meng (meng@cgl.ucsf.edu) escribió:
Hi Fernando, You already calculated the values of Coulombic ESP on the interface: it is displayed. However, I guess you mean that you want to write the values that you have already shown with coloring to some file. There is a “surfval.py” python script in the Chimera scripts page that is supposed to do that, although it may be the whole surface (not just the interface), see: <http://www.cgl.ucsf.edu/trac/chimera/wiki/Scripts>
The Coulombic Surface Coloring tool (and command) also has an option to open the grid of Coulombic ESP values as as separate model. This grid is what is interpolated to get the values for surface coloring. This separate grid model can be saved using the Volume Viewer tool’s File menu. < http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombi...
< http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombi...
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html>
Getting polar/nonpolar surface area is the same question you asked in September. Here were the responses: < http://www.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016139.html
< http://www.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016159.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 30, 2019, at 9:35 AM, Fernando Villa <fer.vdl1928@gmail.com> wrote:
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 1avx display ~longbond split delete 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:
<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
<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 >>>
Dear Fernando, The values are in whatever units are in the map file. So you would look in the documentation for the program that made the map (APBS, DelPhi, …) to find out what the units are. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 2, 2020, at 9:22 PM, Fernando Villa <fer.vdl1928@gmail.com> wrote:
Dear Elaine.
Thank you very much, I really appreciate it. I am confused with some data. A few months ago Tom Goddard sent me a phyton code to get the vertex coordinates and the values in Reply log:
In Windows: 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
To obtain the output vertex coordinates and potential values: Commands: open 1avx display ~ longbond split delete solvent surf # 0.1
Tools> Surface/Binding analysis>Coulombic surface coloring > Check the box compute grid > Apply
Surface color>Click color = All values Appear in reply log (attached file: 001_xyz-val_ESP.txt) <imagen.png> I suppose that the first three numbers are the vertex coordinates and the last value is the ESP Coulombic (Kcal / mol.e).
Value at mouse position:
Surface color> Options > Check the box Report value at mouse position > Click color: <imagen.png> All the electrostatic potential values appear by Coulombic [Kcal / (mol.e)] at the mouse position, I suppose they are the same values shown in replylog = file 001_xyz-val_ENG.txt.
However, when I open the surfval.py script Command: surfvalues # 0.1 # 1 ~/Desktop /002_xyz-val_script-val_ENG.txt
A file is saved (attached file: 002_xyz-val_script-val_ESP.txt) with the same vertex coordinates. The ESP values in Kcal/(mol.e) are different from 001_xyz-val_ESP.txt. <imagen.png>
Besides, if I save the values from Volume viewer: Volume viewer> Tools> Values at atom position
Click Histogram> Render / Select by attribute File> Save attribute> Click box “Restrict save to current selection, if any”> File name: 003_@val_ENG.txt> Save (attached file: 003_@val_ENG.txt) The ESP values --> Kcal/(mol.e)
My question is: The files 001_xyz-val_ESP.txt, 002_xyz-val_script-val_ENP.txt, 003_@val_ESP.txt, and the values at mouse position have units in Kcal/(mol.e)?
If I'm wrong, let me know please.
Regards.
Fer.
El lun., 30 de dic. de 2019 a la(s) 11:56, Elaine Meng (meng@cgl.ucsf.edu) escribió: Hi Fernando, You already calculated the values of Coulombic ESP on the interface: it is displayed. However, I guess you mean that you want to write the values that you have already shown with coloring to some file. There is a “surfval.py” python script in the Chimera scripts page that is supposed to do that, although it may be the whole surface (not just the interface), see: <http://www.cgl.ucsf.edu/trac/chimera/wiki/Scripts>
The Coulombic Surface Coloring tool (and command) also has an option to open the grid of Coulombic ESP values as as separate model. This grid is what is interpolated to get the values for surface coloring. This separate grid model can be saved using the Volume Viewer tool’s File menu. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html#volume> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html>
Getting polar/nonpolar surface area is the same question you asked in September. Here were the responses: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016139.html> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016159.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 30, 2019, at 9:35 AM, Fernando Villa <fer.vdl1928@gmail.com> wrote:
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 1avx display ~longbond split delete 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:
<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
<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
<003_@val_ESP.txt><001_xyz-val_ESP.txt><002_xyz-val_script-val_ESP.txt>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thank you very much Dr. Elaine, it has helped me a lot, I really appreciate it .. best regards. Fer. ATTE Fernando Villa Díaz El vie., 3 de ene. de 2020 a la(s) 11:02, Elaine Meng (meng@cgl.ucsf.edu) escribió:
Dear Fernando, The values are in whatever units are in the map file. So you would look in the documentation for the program that made the map (APBS, DelPhi, …) to find out what the units are. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 2, 2020, at 9:22 PM, Fernando Villa <fer.vdl1928@gmail.com> wrote:
Dear Elaine.
Thank you very much, I really appreciate it. I am confused with some data. A few months ago Tom Goddard sent me a phyton code to get the vertex coordinates and the values in Reply log:
In Windows: 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
To obtain the output vertex coordinates and potential values: Commands: open 1avx display ~ longbond split delete solvent surf # 0.1
Surface color>Click color = All values Appear in reply log (attached file: 001_xyz-val_ESP.txt) <imagen.png> I suppose that the first three numbers are the vertex coordinates and
Tools> Surface/Binding analysis>Coulombic surface coloring > Check the box compute grid > Apply the last value is the ESP Coulombic (Kcal / mol.e).
Value at mouse position:
Surface color> Options > Check the box Report value at mouse position > Click color: <imagen.png> All the electrostatic potential values appear by Coulombic [Kcal / (mol.e)] at the mouse position, I suppose they are the same values shown in replylog = file 001_xyz-val_ENG.txt.
However, when I open the surfval.py script Command: surfvalues # 0.1 # 1 ~/Desktop /002_xyz-val_script-val_ENG.txt
A file is saved (attached file: 002_xyz-val_script-val_ESP.txt) with the same vertex coordinates. The ESP values in Kcal/(mol.e) are different from 001_xyz-val_ESP.txt. <imagen.png>
Besides, if I save the values from Volume viewer: Volume viewer> Tools> Values at atom position
Click Histogram> Render / Select by attribute File> Save attribute> Click box “Restrict save to current selection, if any”> File name: 003_@val_ENG.txt> Save (attached file: 003_@val_ENG.txt) The ESP values --> Kcal/(mol.e)
My question is: The files 001_xyz-val_ESP.txt, 002_xyz-val_script-val_ENP.txt, 003_@val_ESP.txt, and the values at mouse position have units in Kcal/(mol.e)?
If I'm wrong, let me know please.
Regards.
Fer.
El lun., 30 de dic. de 2019 a la(s) 11:56, Elaine Meng ( meng@cgl.ucsf.edu) escribió: Hi Fernando, You already calculated the values of Coulombic ESP on the interface: it is displayed. However, I guess you mean that you want to write the values that you have already shown with coloring to some file. There is a “surfval.py” python script in the Chimera scripts page that is supposed to do that, although it may be the whole surface (not just the interface), see: <http://www.cgl.ucsf.edu/trac/chimera/wiki/Scripts>
The Coulombic Surface Coloring tool (and command) also has an option to open the grid of Coulombic ESP values as as separate model. This grid is what is interpolated to get the values for surface coloring. This separate grid model can be saved using the Volume Viewer tool’s File menu. < http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombi...
< http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombi...
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html>
Getting polar/nonpolar surface area is the same question you asked in September. Here were the responses: < http://www.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016139.html
< http://www.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016159.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 30, 2019, at 9:35 AM, Fernando Villa <fer.vdl1928@gmail.com> wrote:
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 1avx display ~longbond split delete 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:
<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
<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 > >>> > > <003_@val_ESP.txt ><001_xyz-val_ESP.txt><002_xyz-val_script-val_ESP.txt>_______________________________________________ > Chimera-users mailing list: Chimera-users@cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Fernando, The print statement I suggested you add to the Chimera surface color code gives the electrostatic potential values 1.4 Angstroms out from the surface while the surfval.py script from the Chimera Python scripts page gives the values on the surface. The 1.4 Angstrom offset is described in the Surface Color tool documentation https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolo... <https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html> and that offset parameter is shown in the Options panel of the Surface Color dialog. Tom
On Jan 2, 2020, at 9:22 PM, Fernando Villa <fer.vdl1928@gmail.com> wrote:
Dear Elaine.
Thank you very much, I really appreciate it. I am confused with some data. A few months ago Tom Goddard sent me a phyton code to get the vertex coordinates and the values in Reply log:
In Windows: 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
To obtain the output vertex coordinates and potential values: Commands: open 1avx display ~ longbond split delete solvent surf # 0.1
Tools> Surface/Binding analysis>Coulombic surface coloring > Check the box compute grid > Apply
Surface color>Click color = All values Appear in reply log (attached file: 001_xyz-val_ESP.txt) <imagen.png> I suppose that the first three numbers are the vertex coordinates and the last value is the ESP Coulombic (Kcal / mol.e).
Value at mouse position:
Surface color> Options > Check the box Report value at mouse position > Click color: <imagen.png> All the electrostatic potential values appear by Coulombic [Kcal / (mol.e)] at the mouse position, I suppose they are the same values shown in replylog = file 001_xyz-val_ENG.txt.
However, when I open the surfval.py script Command: surfvalues # 0.1 # 1 ~/Desktop /002_xyz-val_script-val_ENG.txt
A file is saved (attached file: 002_xyz-val_script-val_ESP.txt) with the same vertex coordinates. The ESP values in Kcal/(mol.e) are different from 001_xyz-val_ESP.txt. <imagen.png>
Besides, if I save the values from Volume viewer: Volume viewer> Tools> Values at atom position
Click Histogram> Render / Select by attribute File> Save attribute> Click box “Restrict save to current selection, if any”> File name: 003_@val_ENG.txt <mailto:003_@val_eng.txt>> Save (attached file:003_@val_ENG.txt <mailto:003_@val_eng.txt>) The ESP values --> Kcal/(mol.e)
My question is: The files 001_xyz-val_ESP.txt, 002_xyz-val_script-val_ENP.txt, 003_@val_ESP.txt <mailto:003_@val_esp.txt>, and the values at mouse position have units in Kcal/(mol.e)?
If I'm wrong, let me know please.
Regards.
Fer.
El lun., 30 de dic. de 2019 a la(s) 11:56, Elaine Meng (meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>) escribió: Hi Fernando, You already calculated the values of Coulombic ESP on the interface: it is displayed. However, I guess you mean that you want to write the values that you have already shown with coloring to some file. There is a “surfval.py” python script in the Chimera scripts page that is supposed to do that, although it may be the whole surface (not just the interface), see: <http://www.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://www.cgl.ucsf.edu/trac/chimera/wiki/Scripts>>
The Coulombic Surface Coloring tool (and command) also has an option to open the grid of Coulombic ESP values as as separate model. This grid is what is interpolated to get the values for surface coloring. This separate grid model can be saved using the Volume Viewer tool’s File menu. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombi... <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombi... <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html#volume>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html>>
Getting polar/nonpolar surface area is the same question you asked in September. Here were the responses: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016139.html <http://www.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016139.html>> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016159.html <http://www.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016159.html>>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 30, 2019, at 9:35 AM, Fernando Villa <fer.vdl1928@gmail.com <mailto:fer.vdl1928@gmail.com>> wrote:
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 1avx display ~longbond split delete 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:
<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
<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 <mailto: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 <mailto: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 <mailto: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 <mailto: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
<003_@val_ESP.txt><001_xyz-val_ESP.txt><002_xyz-val_script-val_ESP.txt>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
Dear all, running the Autodock Vina module returns a list of docked compounds. The resulting ViewDock table has 2 colums showing RMSD values. What they refer? Thanks for your help, Best regards, Marco -- 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 http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette
https://www.researchgate.net/post/What_is_the_importance_rmsd_ub_and_rmsd_lb... has a good explanation of what they mean. Conrad On 1/9/2020 9:54 AM, Marco Sette wrote:
Dear all,
running the Autodock Vina module returns a list of docked compounds. The resulting ViewDock table has 2 colums showing RMSD values.
What they refer?
Thanks for your help,
Best regards,
Marco
Thanks for the explanations. I was wondering the rmsd values were different from the values obtained by the match command. Now I realise that Vina uses a different approach. Thanks again, Marco Il 09/01/2020 19:29, Conrad Huang ha scritto:
https://www.researchgate.net/post/What_is_the_importance_rmsd_ub_and_rmsd_lb...
has a good explanation of what they mean.
Conrad
On 1/9/2020 9:54 AM, Marco Sette wrote:
Dear all,
running the Autodock Vina module returns a list of docked compounds. The resulting ViewDock table has 2 colums showing RMSD values.
What they refer?
Thanks for your help,
Best regards,
Marco
-- 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 http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette
Hi Marco, This is really an AutoDock Vina question rather than a Chimera question, because Chimera is just showing the values it gets back. See the “Output” section of the AutoDock Vina manual: <http://vina.scripps.edu/manual.html#output> It is also important to realize that the AutoDock Vina web service used by the Chimera tool only allows very little sampling, not sufficient for most research purposes. For more thorough sampling and/or use of other options not available through the Chimera interface, you would need to download and use AutoDock Vina directly (not using Chimera). This is a “boxed warning" on the Chimera manual page for this tool: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 9, 2020, at 9:54 AM, Marco Sette <sette@uniroma2.it> wrote:
Dear all, running the Autodock Vina module returns a list of docked compounds. The resulting ViewDock table has 2 colums showing RMSD values. What they refer? Thanks for your help, Best regards, Marco
participants (5)
-
Conrad Huang -
Elaine Meng -
Fernando Villa -
Marco Sette -
Tom Goddard