How did pymol select the dots of the .opendx file?

[NoMatter-98]

I use apbs and get opendx file, then load it into pymol and show the dots It shows like this:

but how can i select the very part i need? ### Here I need to find the coordination of the white dot. How did you show the opendx file? opendx file contains large mounts of chargeValues, in this case ,the mesh size is 129129161, the opendx file contains every dots' charge value, but when it was loaded into pymol only the protain like part dots were reserved. I changed half(x from 0 to 60 and all the y , z) of the charge value into a specific value and it shows like this:

But i set the chargevalue into 0 ,1,-1, the picture is the same.

I saw the same problem issued by other people in other platform but they seems gave up. It would be very helpful if you could help us solve this question. Thanks a lot!

[NoMatter-98]

Besides I need to color the selected coordinations (for examples into red), and i don't know how to achieve that (ಥ_ಥ) it cannot select the point like pdb or pqr file

[sbembenek18]

I'm not totally clear what you're looking to do, but perhaps this will help a bit.

You've created a DX file (MyDX.dx) from APBS, which has electrostatic potential as it values at the DX grid points. You gave APBS some molecule in order to do this calculation.

In Pymol -->

1) Read in the DX grid -- the box ('extent') should enclose the molecule (which you can optionally read in as well or not).

If you see the dots and you do not want them, you can hide them. Pymol gets the dot info from the molecule you used for the APBS calculation. It's essentially a 'dot surface' around your molecule.

To draw isosurfaces for 'negative' and 'positive', use the isosurface command:

3) isosurface pos_surface, MyDX, 1 4) isosurface neg_surface, MyDX, -1

where MyDX is the name of the DX grid without the '.dx' Now color the the surfaces (e.g., read for the negative and blue for the positive).

As far as selecting individual DX grid points in Pymol, I don't think you can do this -- at least I do not know how. But you could read in your molecule that you used for the APBS calculation and select the atoms related to those portions of the surface or grid points.