Electrostatic potential values at each residue
Dear All, I'd like to get the electrostatic potential (ESP) values at each residue in a protein. I implemented the "Coulombic Surface Coloring", then get the distribution of ESP values at each residue by "Render/Select by Attribute" (Attributes of [residues], Select -> Attribute [value_Coulombic_ESP]). However, The surface plot and the ESP values obtained by "Render/Select by Attribute" do not coincide with each other. For example, there are some residues where the surface plot reports positive ESP values, while "Render/Select by Attribute" gives negative ones (e.g. VAL70 CG2 in the Chimera session file attached.). Could you teach me how to solve this discrepancy? Thank you very much in advance, T.M.
Hi T.M., I think you've left out details about what you have done -- how did you get this value_Coulombic_ESP attribute? Did you use values at atom positions? Did you use the "compute grid" option in the Coulombic Surface Coloring dialog? I guess you did that. And you say you use Attributes of Residues -- is that an average of the atom attribute obtained from the values at atom positions dialog? I can't be sure what you've done, but here's a guess at what your problem is. The Chimera Coulombic Surface Coloring dialog computes the potential at points 1.4 Angstroms out from the solvent excluded molecular surface and colors the surface points using that value. If you instead use a potential value interpolated at the center of an atom, that will give a much different value -- in fact it should tend to give an extremely large value because if the atom is charged the potential at the atom center is infinite using the simple Coulomb calculation. But because you are (I think) using a value interpolated from a grid you don't get an infinite value, just a very large value. So I think your problem is you are not considering that the electrostatic potential varies rapidly in space and you are comparing colors using potential values at different positions in space. Tom On Dec 2, 2013, at 6:31 PM, Tatsuhito Matsuo wrote:
Dear All,
I'd like to get the electrostatic potential (ESP) values at each residue in a protein. I implemented the "Coulombic Surface Coloring", then get the distribution of ESP values at each residue by "Render/Select by Attribute" (Attributes of [residues], Select -> Attribute [value_Coulombic_ESP]). However, The surface plot and the ESP values obtained by "Render/Select by Attribute" do not coincide with each other. For example, there are some residues where the surface plot reports positive ESP values, while "Render/Select by Attribute" gives negative ones (e.g. VAL70 CG2 in the Chimera session file attached.). Could you teach me how to solve this discrepancy?
Thank you very much in advance,
T.M.
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Dear TM, The values are for different locations: the attributes are values mapped to atomic centers, whereas the surface coloring shows the potential values farther out, at the surface or beyond (even farther from the atom centers). By default in Chimera, Coulombic or other electrostatic surface coloring shows the values at points 1.4 angstroms outward from the displayed (solvent-excluded) surface, approximating the values at the larger solvent-accessible surface, which is not displayed. This is the "Distance from surface" parameter in the Coulombic surface coloring dialog, and there is a similar option in the Surface Color tool. Using the Coulombic coloring tool does not automatically create attributes. I'm guessing you used the option to create a grid, then read in the grid, and then used Values at Atom Positions to get the attributes assigned. (Your session cannot be restored because it also requires the grid file.) To summarize, however, you would not expect the values to be the same because the locations where the potential is evaluated are quite different. I hope this helps, 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 Dec 2, 2013, at 6:31 PM, Tatsuhito Matsuo wrote:
Dear All,
I'd like to get the electrostatic potential (ESP) values at each residue in a protein. I implemented the "Coulombic Surface Coloring", then get the distribution of ESP values at each residue by "Render/Select by Attribute" (Attributes of [residues], Select -> Attribute [value_Coulombic_ESP]). However, The surface plot and the ESP values obtained by "Render/Select by Attribute" do not coincide with each other. For example, there are some residues where the surface plot reports positive ESP values, while "Render/Select by Attribute" gives negative ones (e.g. VAL70 CG2 in the Chimera session file attached.). Could you teach me how to solve this discrepancy?
Thank you very much in advance,
T.M.
Dear Dr. Meng, Thank you very much for the reply and I'm sorry for lacking of the necessary file to open the session I attached. My question was solved thanks to your clear explanation and I now see that I misunderstood the ESP attributes. Thank you so much for your help. Best wishes, T.M. On 2013/12/05, at 2:37, Elaine Meng wrote:
Dear TM, The values are for different locations: the attributes are values mapped to atomic centers, whereas the surface coloring shows the potential values farther out, at the surface or beyond (even farther from the atom centers). By default in Chimera, Coulombic or other electrostatic surface coloring shows the values at points 1.4 angstroms outward from the displayed (solvent-excluded) surface, approximating the values at the larger solvent-accessible surface, which is not displayed. This is the "Distance from surface" parameter in the Coulombic surface coloring dialog, and there is a similar option in the Surface Color tool.
Using the Coulombic coloring tool does not automatically create attributes. I'm guessing you used the option to create a grid, then read in the grid, and then used Values at Atom Positions to get the attributes assigned. (Your session cannot be restored because it also requires the grid file.)
To summarize, however, you would not expect the values to be the same because the locations where the potential is evaluated are quite different.
I hope this helps, 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 Dec 2, 2013, at 6:31 PM, Tatsuhito Matsuo wrote:
Dear All,
I'd like to get the electrostatic potential (ESP) values at each residue in a protein. I implemented the "Coulombic Surface Coloring", then get the distribution of ESP values at each residue by "Render/Select by Attribute" (Attributes of [residues], Select -> Attribute [value_Coulombic_ESP]). However, The surface plot and the ESP values obtained by "Render/Select by Attribute" do not coincide with each other. For example, there are some residues where the surface plot reports positive ESP values, while "Render/Select by Attribute" gives negative ones (e.g. VAL70 CG2 in the Chimera session file attached.). Could you teach me how to solve this discrepancy?
Thank you very much in advance,
T.M.
participants (3)
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Elaine Meng -
Tatsuhito Matsuo -
Tom Goddard