Hi Osvaldo, Thank you for your suggestion! Today I tried the APBS again and it works this time. Just right after reading your email, I think I've figured out what the problem is. I think the molecule must be in the same location for both calculation and rendering. I guess last time, I used different files. Even they are the exactly same molecules, somehow in pymol the locations of molecules are not aligned. For example I have two files A and B which are the identical molecules but not aligned. If I used A to do APBS calculation, but opened the output with B, it will be completely white. If I aligned B with A first, and save B as a new pdb file B'. I am able to render the colors in B' with the original APBS output I calculated from A.
Best, Xiao 2015-07-26 15:30 GMT-07:00 Osvaldo Martin <aloctavo...@gmail.com>: > Hi Victor, > > You should never use the build-in "generate vacuum electrostatic > potential" function for any real analysis. The theoretically correct > approach is to use the Poisson-Boltzman equation (as implemented for > example in the APBS plugin). Other approaches like generalized Born models > or SASA methods can be justified for things like Molecular Dynamics, i.e. > when you need to compute the electrostatic energy contributions very often > (at expense of reducing the accuracy of your computations). > Could you provide an example of your "white" molecules? I would like to > see if I can reproduce your observation. > > > Cheers, > Osvaldo. > > > > On Sun, Jul 26, 2015 at 3:48 AM, Victor Xiao <victor41...@gmail.com> > wrote: > >> Dear All, >> >> First, I am trying to compare surface electrostatic potential among >> several members from a protein family. I was able to use build-in function >> in pymol (generate vacuum electrostatic potential). However, the range of >> potential for each molecule is automatically set up and they are different. >> (e.g, one could be -5 to 5 and another one could be -10 to 10, so the color >> scales between these two molecule are not comparable. A -5 potential will >> be compeletely red in the first molecule, but is only light red in the >> second molecule). Can I set the potential to the same range in order to >> compare? >> >> Second, a off-topic question, I also tried to use APBS calculation. By >> this way I was able to render most of molecules in red-white-blue scale, >> but a few of molecules are completely white. I couldn't find where the >> problem is. >> >> >> Any comment or suggestion will be appreciated. Thank you very much! >> >> Best, >> Xiao >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> > >
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