Adsorption density distribution map

[Z.GAO]

Hi everyone,

In the post-processing of gas adsorption MOF, I want to make an adsorption density distribution map. MOF is a triclinic system, and the adsorption density map drawn by VisIt software is still a cubic structure. So I use iRASPA software to draw it. Although iRASPA can show the triclinic structure, there is no color scale, only one color, which makes it difficult to intuitively judge the priority adsorption site. How can I solve this problem?

In addition, when I use iRASPA to present the molecular structure, I find that some atoms are not bonded. How should I deal with this?

Best wishes!

Zheng

[David Dubbeldam]

You probably used "surface"-rendering. With "volume-rendering" you can get more of a color-gradient.
Bonding is controlled by a general rule, also employed by VMD: The radius < (covalent radius of atom1 + atom2 + 0.56).