Multiwfn forum

Hans

Member

Registered: 2018-10-24

Posts: 10

Atom colors and Cue Mode effect in VMD

When viewing the molecular structure in VMD, it shows the atoms with default colors (eg Nitrogen from blue and oxygen from red), my question is is it possible to change these default colors in VMD to other custom colors? Is it possible to do this by means of a script? (Fig. 1).

Another problem that I have when visualizing a molecule in VMD is that when applying the PERSPECTIVE effect and additionally the CUE MODE-LINEAR effect, I do not obtain this last effect in the visualization of the molecule (Fig. 2), the values that I use for this effect they are Cue Start = 1.5 and Cue End = 2.75, I tried various values but did not get the desired effect.

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,830

Website

Re: Atom colors and Cue Mode effect in VMD

1 You can change default color by editing [VMD folder]\scripts\vmd\colordefs.dat

2 You should choose "Display" - "Depth Cueing" to enable depth cueing effect, otherwise cue mode setting will not take effect

Louischarlc0

Member

Registered: 2020-07-21

Posts: 65

Re: Atom colors and Cue Mode effect in VMD

Hi there

I'm trying to plot the fluorescence spectra in multiwfn. The manual says that it can be plotted in exactly the same manner as UV-Vis spectra other than considering Kasha's rule. However, I'm not sure which parameters to change. Should I adjust the oscillator strength?

Thanks in advance

Regards
Louis-Charl

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,830

Website

Re: Atom colors and Cue Mode effect in VMD

Hi there

I'm trying to plot the fluorescence spectra in multiwfn. The manual says that it can be plotted in exactly the same manner as UV-Vis spectra other than considering Kasha's rule. However, I'm not sure which parameters to change. Should I adjust the oscillator strength?

Thanks in advance

Regards
Louis-Charl

Hello,

I have updated Multiwfn manual on Multiwfn website, a new section 4.11.11 has been added, which illustrated how to use Multiwfn to plot fluorescence spectrum for BODIPY molecule. Please check it.

Best regards,

Tian

Louischarlc0

Member

Registered: 2020-07-21

Posts: 65

Re: Atom colors and Cue Mode effect in VMD

Thank you so much. I will read over it.

Regards
Louis-Charl

Abdullah

Member

Registered: 2021-01-28

Posts: 32

Re: Atom colors and Cue Mode effect in VMD

There are only 33 named colors in VMD. Is this possible to set unique color for all elements in periodic table, ideally same color for each element as in Gaussview?

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,830

Website

Re: Atom colors and Cue Mode effect in VMD

There are only 33 named colors in VMD. Is this possible to set unique color for all elements in periodic table, ideally same color for each element as in Gaussview?

Please view my blog article http://sobereva.com/652 (written in Chinese, please use Google translator)