Display atoms after multiscale model
Hello, I am working on a virus capsid and trying to figure out the buried surface area between subunits (similar to what ViperDB has. I have to do this for a few capsids and I am trying to automate this to the maximum possible extent. I have been able to follow the steps in this link Buried surface area calculation <http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-December/001131.html> and manually calculate the information. Are there commands available to do the same? Also, what is the difference between the surfaces created using a multiscale model and surfaces computed from the atom-spec? Would this difference in the surface affect the calculation of the buried surface area? And if it does affect it which one be a more accurate representation? Thank you Vamsee
Hi Vamsee, Now there is a “measure buriedArea” command, so it should be much simpler. However, you have to make sure that atoms are loaded for the subunits of interest, not just the low-resolution multiscale surfaces, and be very careful to specify only the intended atoms in the command (for example, you might want to delete any water, ligands, etc. first to make it easier). Even though the displayed molecular surface would automatically exclude stuff like water, the buried area calculation does not. <www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedArea> The Multiscale low-resolution surfaces are calculated differently and would have a different surface area than the standard molecular surfaces (measure buriedArea calculates the standard ones). Seems logical that the results with low resolution surfaces would be less accurate. See the Multiscale documentation, especially the sections “low-res surfaces” and “loading atomic coordinates”: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html> 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 Oct 29, 2014, at 2:15 PM, vamsee <vamseedharr@gmail.com> wrote:
Hello, I am working on a virus capsid and trying to figure out the buried surface area between subunits (similar to what ViperDB has. I have to do this for a few capsids and I am trying to automate this to the maximum possible extent. I have been able to follow the steps in this link Buried surface area calculation and manually calculate the information. Are there commands available to do the same? Also, what is the difference between the surfaces created using a multiscale model and surfaces computed from the atom-spec? Would this difference in the surface affect the calculation of the buried surface area? And if it does affect it which one be a more accurate representation? Thank you Vamsee
Hi Elaine, I have been trying to calculate SASA of some multimeric proteins and in certain cases negative values come up. Is there an explanation to this? Is it actually telling me something about the surface area and is there workaround to getting the actual values? Thank you Vamsee On Wed, Oct 29, 2014 at 8:01 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Vamsee, Now there is a “measure buriedArea” command, so it should be much simpler. However, you have to make sure that atoms are loaded for the subunits of interest, not just the low-resolution multiscale surfaces, and be very careful to specify only the intended atoms in the command (for example, you might want to delete any water, ligands, etc. first to make it easier). Even though the displayed molecular surface would automatically exclude stuff like water, the buried area calculation does not.
<www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedArea>
The Multiscale low-resolution surfaces are calculated differently and would have a different surface area than the standard molecular surfaces (measure buriedArea calculates the standard ones). Seems logical that the results with low resolution surfaces would be less accurate. See the Multiscale documentation, especially the sections “low-res surfaces” and “loading atomic coordinates”:
< http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemu...
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 Oct 29, 2014, at 2:15 PM, vamsee <vamseedharr@gmail.com> wrote:
Hello, I am working on a virus capsid and trying to figure out the buried surface area between subunits (similar to what ViperDB has. I have to do this for a few capsids and I am trying to automate this to the maximum possible extent. I have been able to follow the steps in this link Buried surface area calculation and manually calculate the information. Are there commands available to do the same? Also, what is the difference between the surfaces created using a multiscale model and surfaces computed from the atom-spec? Would this difference in the surface affect the calculation of the buried surface area? And if it does affect it which one be a more accurate representation? Thank you Vamsee
Hi Vamsee, As far as I know it's not possible to get negative SASA, but probably you meant negative buried SASA since that's what we were talking about before. If the negative values are close to zero, it may be just rounding. However, if they are larger in magnitude, it may mean there was some failure in part of the calculation, as discussed in this earlier post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-April/005119.html> There should be some message in the Reply Log if there was such a problem. You could try using slightly different values of probeRadius and/or vertexDensity in the "measure buriedArea" command to see if it can be avoided. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedArea> Also best to do these calculations without hydrogens (i.e. if they are present, delete them beforehand). Also, make sure you are not trying to do this with any CA-only structures, as they are not suitable for any surface area calculations. Well, those are all of my ideas. 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 1, 2014, at 10:45 AM, vamsee <vamseedharr@gmail.com> wrote:
Hi Elaine, I have been trying to calculate SASA of some multimeric proteins and in certain cases negative values come up. Is there an explanation to this? Is it actually telling me something about the surface area and is there workaround to getting the actual values? Thank you Vamsee
On Wed, Oct 29, 2014 at 8:01 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Vamsee, Now there is a “measure buriedArea” command, so it should be much simpler. However, you have to make sure that atoms are loaded for the subunits of interest, not just the low-resolution multiscale surfaces, and be very careful to specify only the intended atoms in the command (for example, you might want to delete any water, ligands, etc. first to make it easier). Even though the displayed molecular surface would automatically exclude stuff like water, the buried area calculation does not.
<www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedArea>
The Multiscale low-resolution surfaces are calculated differently and would have a different surface area than the standard molecular surfaces (measure buriedArea calculates the standard ones). Seems logical that the results with low resolution surfaces would be less accurate. See the Multiscale documentation, especially the sections “low-res surfaces” and “loading atomic coordinates”:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html>
I hope this helps, Elaine
On Oct 29, 2014, at 2:15 PM, vamsee <vamseedharr@gmail.com> wrote:
Hello, I am working on a virus capsid and trying to figure out the buried surface area between subunits (similar to what ViperDB has. I have to do this for a few capsids and I am trying to automate this to the maximum possible extent. I have been able to follow the steps in this link Buried surface area calculation and manually calculate the information. Are there commands available to do the same? Also, what is the difference between the surfaces created using a multiscale model and surfaces computed from the atom-spec? Would this difference in the surface affect the calculation of the buried surface area? And if it does affect it which one be a more accurate representation? Thank you Vamsee
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