AlphaFold colouring of models predicted outside of ChimeraX
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.
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://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#coloring> ...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://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#bfactor> ...and palette options <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options> 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@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.
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@cgl.ucsf.edu> Date: Wednesday, 11 May 2022 at 9:48 am To: James Hodgkinson-Bean <hodja191@student.otago.ac.nz> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@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@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.
participants (2)
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Elaine Meng -
James Hodgkinson-Bean