Color a protein by C-alpha RMSD using ChimeraX
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- เผยแพร่เมื่อ 4 ต.ค. 2024
- We show how to color the residues of two aligned proteins according to how far apart their corresponding backbone C-alpha atoms are using ChimeraX version 1.6. The example shown compares an archaeal crenactin protein to a rabbit actin.
Great, thank you! How does one actually see the RMSD numerical values for each residue?
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
Hi, very helpful video. But can please also make a video on how to save this structure in .mmcif or .pdb format. Thank you.
Hi, thank you for the tutorial. I can't find the tool "render by attribute" , is there any command line to do that?
The render by attribute tool is in ChimeraX version 1.6. You must be using an older ChimeraX.
Does anyone know if you can use ChimeraX with Autodock Vina
Is it possible to align on one chain but colour all chain relative to their rmsd to chains with the same ID?
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.
@@SurfaceColor Amazing, it works perfectly and will save me so much time!!
@@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!
@@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".