Open eloyvallinaes opened 1 year ago
I commend you for giving that a go. But I honestly can't give you a solid or helpful answer for this as it'll be pure conjecture. I haven't delved too much into the code (because frankly it's a lot).
This is my best guess just from cursory view from where the coloring is done. There does seem to be a lot of interpolation and smoothing happening with close neighbors especially in the last file here, but I am not aware really what the broad algorithm is.
https://github.com/schrodinger/pymol-open-source/blob/master/layer2/RepSurface.cpp#L2171 https://github.com/schrodinger/pymol-open-source/blob/master/layer1/Color.cpp#L191 https://github.com/schrodinger/pymol-open-source/blob/master/layer2/ObjectGadgetRamp.cpp#L470
I am working with APBS calculations on a set of interesting proteins. Briefly, what I want is an explicit representation of the potential at the protein's solvent accessible surface area—that is the actual numbers, not just the coloured surface. This entails:
This is in many ways equivalent to the first example in the pymol docs for
ramp_new
: https://pymolwiki.org/index.php/Ramp_New#Examples. It feels like that command pulls quite a lot of weight, so I am wondering: what isramp_new
doing exactly? My guess was that values from the APBS solution grid (.dx
) were being mapped to the faces or the vertices of the surface by some simple nearest-neighbour type of search, with a k-d tree or some other sort of structure, but I am not getting the same results aspymol
gets withramp_new
.I suspect the reason why my trivial solution doesn't work is because ramp_new performs some sort of smoothing over multiple neighbours—how many neighbours? how are they smoothed?—or that pymol's surfaces are much more dense than the solution grid—how many vertices? Sadly, I don't think these details are documented anywhere.
Below is an example of the type of results I am seeing with a small protein:
![pymol_ramp](https://user-images.githubusercontent.com/17429572/194866730-8f783471-6299-4706-a3d0-738972d38118.png)
Left my solution. A noisy surface, with abrupt changes in potential. Right pymol's smoother, more reasonable, less complicated surface. Protein is chain I (trypsin inhibitor) in PDB structure 1TPA. In both images, the same
.dx
file containing the APBS electrostatic potential solution grid is being used.Many thanks!