Question about the protein viewer

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Zangetsu
Posts: 10
Joined: Mon Dec 23, 2019 9:56 pm

Question about the protein viewer

Post by Zangetsu »

Hi all,
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I was wondering what the different colors mean in the viewer, i thought it was as following:
red :O
Black: C
Purple: H
Yellow: S

But if i think about it like this , it doesn't add up...
I have a Benzene ring (H?) what i have marked, and to the right of it a red one that has 3 bonds
and even an -CH-CO2 part that doesn't switch between an C=COOH , just remains static as a CH-CO2 (with O no H on it),
Can any of you wizards explain to me what particle is what atom ?:D
Brad_C
Posts: 8
Joined: Sat Apr 18, 2020 10:01 pm

Re: Question about the protein viewer

Post by Brad_C »

The FAH client using the OPENMM core (which runs on GPUs) is not sending correct atom types to the viewer. So the colors don't mean much. Atom types from the GROMACS core are ok, colors are C=dark gray, H=light gray, O=red, N=blue, S=yellow.
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toTOW
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Re: Question about the protein viewer

Post by toTOW »

The whole scheme used in the viewer is explained here : https://en.wikipedia.org/wiki/CPK_coloring

On FAH, the purple atoms are "heavy" hydrogen.
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