Color a protein by C-alpha RMSD using ChimeraX

[@professorswenson3504]

Great, thank you! How does one actually see the RMSD numerical values for each residue?

[@wubishetmtadesset4225]

Great video for us, the beginners. But I missed the home toolbar ...to say I couldn't see graphic contents for the tasks on the version I am using. Each time I have to go the menu and drop down to find those. Can anybody help how to bring it back? Thanks

[@krupapatel9761]

Hi, very helpful video. But can please also make a video on how to save this structure in .mmcif or .pdb format. Thank you.

[@remiruedas4501]

Hi, thank you for the tutorial. I can't find the tool "render by attribute" , is there any command line to do that?

[@SurfaceColor]

The render by attribute tool is in ChimeraX version 1.6. You must be using an older ChimeraX.

[@pimientopicante3870]

Does anyone know if you can use ChimeraX with Autodock Vina

[@danielmihailov8794]

Is it possible to align on one chain but colour all chain relative to their rmsd to chains with the same ID?

[@SurfaceColor]

Yes. Say you aligned on chain A as in the video, and now you want to color chain B by C-alpha RMSD. It is simple if the your B chains all have the same sequence so no sequence alignment is needed -- in that case use command "sequence chain /B" to show the sequence will all the B chains associated, then show the Calpha RMSD header (right click in sequence panel, menu Headers / Ca RMSD), then color as in the video. If the chain B sequences are different then show the sequence for one of the "sequence chain #1/B" then associate the others "sequence associate #2-5/B", then show the Calpha header and proceed as in the video. The "associate" step does a sequence alignment.

[@danielmihailov8794]

@@SurfaceColor Amazing, it works perfectly and will save me so much time!!

[@danielmihailov8794]

@@SurfaceColor Thanks so much for the help! I just have one more question, is it possible to do this if the chain length is not the same? The sequence chain /A command doesn't work if I have slightly different chain As e.g 3-4 amino acids difference. Is there a way around this? I am aligning on chain X with matchmaker #1/X to #2/X and then using this alignment sequence chain /A doesn't work if chains are not the same. If I use matchmaker #1/A to #2/A show true it works but then the alignment is not fixed for all chains and changes if I do the same for all chains. Thanks so much!

[@SurfaceColor]

@@danielmihailov8794 Right. If there is more than one model with a chain /A and the sequences are different then "sequence chain /A" does not work. That only works if the sequences are identical. If the sequences differ, then you show one of them "sequence chain #1/A" and then associate the other chains with that one by right click on the sequence panel and choosing menu entry Structure / Associations.... Then associate each of the other chain /A sequences. This will do a sequence alignment to match them up and it is ok if the sequences are a bit different. Or maybe easier than using the menu is to use command "sequence associate /A".