Question about the protein viewer

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Question about the protein viewer

Postby Zangetsu » Sun Jun 28, 2020 11:15 am

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
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Re: Question about the protein viewer

Postby Brad_C » Mon Jun 29, 2020 7:45 pm

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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Re: Question about the protein viewer

Postby toTOW » Sun Jul 05, 2020 9:04 pm

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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