communities not colored on the struct and struct is not tube, VMD

[Tamas Hegedus]

Hi,

My bio3D is at 2.4.3

vmd(net, pdb, …) results in a vmd.net file, which does not set the colors of the residues based on communities and it also does not render the structure to tube as written in the docs. Only draw sphere and draw cylinder and draw color for these objects are in the vmd.net file.

It would be important to visualize the community colors also on the protein structure - as in the fig of “The vmd() output for the HIVpr example MD trajectory”:

Should I try an earlier version of bio3D?

Thanks for your help,
Tamas

[Xinqiu Yao]

Hi,

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Did you try to change the ‘representation’ to tube and ‘coloring method’ to ‘chain’ in VMD?