[chimerax-users] AlphaFold colouring of models predicted outside of ChimeraX

[James Hodgkinson-Bean]

Hi Elaine

I had tried this command on a previous alphafold model and it didn’t work, but I just tried it then and it appears to be working now!

Thanks so much 😊

Cheers,
James.

From: Elaine Meng <meng at cgl.ucsf.edu>
Date: Wednesday, 11 May 2022 at 9:48 am
To: James Hodgkinson-Bean <hodja191 at student.otago.ac.nz>
Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] AlphaFold colouring of models predicted outside of ChimeraX
Hi James,
I don't have such a structure handy but I believe so, assuming that the confidence values are written to the bfactor field of the resulting PDB file.  In that case you can use command:

color bfactor palette alphafold

...as mentioned here (and there is also an example command for drawing a color key if you want that too)
<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Falphafold.html%23coloring&data=05%7C01%7Chodja191%40student.otago.ac.nz%7Cc6bbfb0fe04642c5b31908da32cece1f%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637878161066632139%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=e6HcFLOR7boS8AHvkMpssLTI0NssUNe4i%2BC6ZWbJKck%3D&reserved=0>

...or if you have other models open and you only wanted to apply this coloring to a specific one, say #1:

color bfactor #1 palette alphafold

See also "color bfactor"
<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fcolor.html%23bfactor&data=05%7C01%7Chodja191%40student.otago.ac.nz%7Cc6bbfb0fe04642c5b31908da32cece1f%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637878161066632139%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=G86t92HGLS8aCN2oPRXxz%2BMhLaF0FjQeB0bSKYeiylo%3D&reserved=0>
...and palette options
<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fcolor.html%23palette-options&data=05%7C01%7Chodja191%40student.otago.ac.nz%7Cc6bbfb0fe04642c5b31908da32cece1f%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637878161066632139%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=wkN0RNRDchl9%2Bi9ULCsEc1hbhHHyM%2BEBAZ1iZp%2BumeA%3D&reserved=0>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 10, 2022, at 2:13 PM, James Hodgkinson-Bean via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>
> Hi
> Recently I’ve been performing batch AlphaFold predictions on colab. I was wondering if it’s possible to apply the confidence colour pallete to these structures in chimera if they have not been predicted in ChimeraX directly?
> Thanks,
> James.
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