NCI plot Isosurface color scheme

[shwetaphd]

Hi @aoterodelaroza

How can we plot the NCI plot (RDG vs lamda2.rho) with an isosurface color scheme/bar with it for a periodic solid? I wanted to see the color of the isosurface that I have obtained corresponds to which rho value in the plot of RDG and rho?

Also, Is there any specific range of rho that corresponds to steric or covalent interaction? I read that value close to zero is considered a vdW interaction but how much close to zero should be considered? Since the color of the isosurface is set manually by setting rho, I am confused about what rho value should be set to properly assign the type of interaction. Your assistance is greatly appreciated!

Thank you.

[528012]

Hello, I also have this question, I want to ask if you know the answer?

[aoterodelaroza]

The first question is related to VMD and the second should be solved by the literature. I left this open in case anyone wants to chime in with an answer or an opinion, although these pages are for critic2 issues. I do not know how to make a colorbar in VMD and I don't think there is a specific range of rho for covalent/steric/vdW interactions.

[aoterodelaroza]

Apparently, there is a way to add a colorbar to the plot in VMD: Extensions -> Visualizations -> Color Scale Bar. Maybe that could be a way.

[528012]

你好

我们如何绘制周期性实体的 NCI 图 （RDG vs lamda2.rho） 和等值面配色方案/条形图？我想查看我获得的等值面的颜色对应于 RDG 和 rho 图中的哪个 rho 值？

另外，是否有任何对应于空间或共价相互作用的特定 rho 范围？我读到接近零的值被视为 vdW 交互、但应该考虑多少接近零？由于等值面的颜色是通过设置 rho 手动设置的，因此我对应该设置什么 rho 值才能正确分配交互类型感到困惑。非常感谢您的帮助！

谢谢。

Hello, I would like to ask why you chose the second largest eigenvalue? lamda2

[528012]

显然，有一种方法可以在 VMD 中的绘图中添加颜色条： 扩展 -> 可视化 -> 色标条。也许这可能是一种方式。
ok Okay, I'll find out