Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture.
The created surface from an electron density calculation is offset in x,y,z and no longer centred on the molecule position. See the attached screen-shot.
I assume you calculate the density on a grid basis in boxes of dx,dy,dz, but do not show it at the center of the boxes position dx/2, dy/2, dz/2.
The created surface from an electron density calculation is offset in x,y,z and no longer centred on the molecule position. See the attached screen-shot. I assume you calculate the density on a grid basis in boxes of dx,dy,dz, but do not show it at the center of the boxes position dx/2, dy/2, dz/2.
Reported by: quantumatoms