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<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US">Hi Elaine<br>
<br>
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!<br>
<br>
Thanks so much </span><span style="font-size:11.0pt;font-family:"Apple Color Emoji";mso-fareast-language:EN-US">😊</span><span style="font-size:11.0pt;mso-fareast-language:EN-US">
<br>
<br>
Cheers, <br>
James. <o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Date: </b>Wednesday, 11 May 2022 at 9:48 am<br>
<b>To: </b>James Hodgkinson-Bean <hodja191@student.otago.ac.nz><br>
<b>Cc: </b>chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject: </b>Re: [chimerax-users] AlphaFold colouring of models predicted outside of ChimeraX<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:11.0pt">Hi James,<br>
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:<br>
<br>
color bfactor palette alphafold<br>
<br>
...as mentioned here (and there is also an example command for drawing a color key if you want that too)<br>
<<a href="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">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</a>><br>
<br>
...or if you have other models open and you only wanted to apply this coloring to a specific one, say #1:<br>
<br>
color bfactor #1 palette alphafold<br>
<br>
See also "color bfactor"<br>
<<a href="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">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</a>><br>
...and palette options<br>
<<a href="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">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</a>><br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On May 10, 2022, at 2:13 PM, James Hodgkinson-Bean via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br>
> <br>
> Hi<br>
> 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?<br>
> Thanks, <br>
> James. <o:p></o:p></span></p>
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