Re: [PyMOL] [Pymol] Set scale of vacuum electrostatic potential

2015-07-27 Thread Victor Xiao
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 differe

Re: [PyMOL] [Pymol] Set scale of vacuum electrostatic potential

2015-07-26 Thread Osvaldo Martin
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 m