Good video. But I have around 100 different protein sequences, so how to automate this prediction? Can we paste all the 100 sequences in one single prediction by a separator? Can you suggest me a solution to do for multiple sequences?
I tried running a protein complex (TOM70 + HSP90alpha x2 + Cullin 5 + SARS-CoV-2 ORF9b) that researchers in a published study ran on Alphafold2. But the results I got look absolutely nothing like their results. Is this a a result of using ChimeraX? I only know how to use Alphafold using ChimeraX. Does anyone know of a good guide for using Alphafold on protein complexes without using ChimeraX?
Hi, thank you for this tutorial. It is instrumental. I have a question. Could you please tell me how to export PAE plot from Chimerax with the label of residue no. in the X and Y axis? Or any method you can think of exporting/visualizing PAE? I think it will be useful to use PAE to present and explain the interaction of the two chains. many thanks!
Great video- Is there any reason you selected 8 as distance between /A and /B (two interacting proteins)? what is the range that we can consider as confident distance? can we go up to 15 ?
I am guessing that confidence is because the protein you are looking at was published in pdb before alphafold2 was trained. I watched a presentation from the alfafold team and they said that would give a false level of confidence just like what you are showing. Those alpha helices and trimeric alignments should not be that high.
Can the distances be measured for a trimer or can you only label distances between two proteins at once? Also What does the PAE domain coloring mean? I know the color key for pLDDDT but not for PAE domains.
Thank you so much for the great tutorial. What is your standard for increasing or decreasing C-alpha distance to color the structure that is different between the Alphafold prediction and the experimental one?
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
Thanks for the helpful video. Is it possible to let AlphaFold predict interactions of two proteins where I already have the .pdb file? Especially if my two proteins would exceed the 1000 residue GPU limit, could this help to circumvent the prediction limitation?
Is there a difference in GPU resource access when using pay-as-you-go versus subscription? I wonder because after buying 100 units without a subscription, the A100 was unavailable (although I could select it). Thanks.
How do you open PAE data from a model created by AlphaColab on Chimera? After I upload the 'predicted_aligned_error_v1.json" JSON file', I get an error saying JSON file 'X' is not AlphaFold predicted aligned error data, expected a top level list PAE file suffix must be ".json" or ".pkl".
Hi, Very very nice explanations, indeed, I know that this video is not new but I've seen it just today. I have a quetsion, I use version 1.6.1 (2023-05-09) of Chimera X and I would like to know how to proceed to run colabfold (now it is the 1.5.2) there is only the command alphafold on this version, in th ebeginning of your video you said that you modified chimera to do this. So, how to do that is my naive question. Thanks a lot, Didier
My protein is above 3000 Amino acid sequence, and it's full pdb structure is not available, what you recommend which server / tool should I use , please reply?
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 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".
I tried using colab for multimer . I paid for colab pro . Structures, plot everything were done but it's not downloading. ! In one structure (1700 amino acids) , I lost 50 units out of 100. And there is no visible solution to get the zip file. . If you know any solution for it, would u please share .
Glad you found the video useful. ChimeraX uses ColabFold which is an optimized version of AlphaFold and you can also run ColabFold without ChimeraX using their web page colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb. Setting up AlphaFold on your own computer is a lot of trouble, requiring Linux, Docker, about 3 Tbytes of free disk and days to download databases, and hopefully a high-end Nvidia GPU, and even after all that work it is 10 times slower than ColabFold. So thanks should go to the developers of ColabFold.
Hi! Great explanation, thanks for showing the error plot function. I have version 1.5 but when I type the command for contacts between the two chains it says 'No residues specified for alphafold contacts'. Could you help me, what am I doing wrong? My guess is that it doesn't recognize that there are two separate chains? Another question: I am not really satisfied with the position in which my protein A is now docked to the other, because I know from literature as well as from experiments I did in the lab that the binding is at a different domain... So would you recommend running alphafold again with some restrictions? Or, if I want try the docking manually: how can I separate the two strands?
The command used in the demonstration is "alphafold contacts /A to /B distance 8" which finds contacts between chain A and chain B. Your data probably uses other chain names (e.g. C and D) and so if you don't modify the command it says no residues were specified. For your second question, if AlphaFold does not predict the complex correctly there are no options to make it give a different result. You could predict each protein separately then open them and move one relative to the other by hand with the "Move model" mouse mode. If you have further questions ask on the ChimeraX mailing list.
Thanks those who built such an amazing program and definitely much helpful for every researchers globally. The very good thing about this software is is no barrier to use it. Non discriminatory at all. Much thankful.
Excellent videos. But I don't understand PAE plot. It would be helpful if you said a little more about it. For example, choose some points in the plot and say exactly what they mean
The PAE values are defined by AlphaFold and described in their publications and is not too intuitive. I have a brief explanation here www.rbvi.ucsf.edu/chimerax/data/pae-apr2022/pae.html. Unfortunately the videos reach more people if they are shorter and do not try to cover all the background material since typical viewers have a short attention span. So my aim in future videos is more along the lines of reducing the content so it can benefit more researchers rather than expanding it.
Thanks so much for this helpful video and clear explanation! I just wonder why you predicted two proteins? Do you think this can predict ligand bind to the protein? Such as to see if ligand bind or not to the target protein? Many thanks
Most proteins function as part of multi-protein complexes, so it is useful to predict complexes of more than one protein. AlphaFold cannot make predictions with ligands, ions, solvent, nucleic acids. It only handles the 20 standard (unmodified) amino acids.
Hi. First, thanks for all of the helpful videos that ChimeraX puts out to use this great software. I really enjoy using it, especially with the Colabfold features added in. Second, is there a way to access the sequence alignments that Colabfold finds for your protein sequences at the beginning of the structure prediction? It would be nice to see which organisms these alignments are coming from and be able to analyze in greater detail the sequence variation.
I used ChimeraX 1.5 in the video (from November 2022). Maybe you are using an old ChimeraX? The version is listed at the top of the Log panel when you start the program. To report the C-alpha RMSD the sequence has to be associated with more than one copy of the structure. Right click on the sequence shows a menu with an entry Structure / Associations that lets you associate multiple structures with the shown sequence if it is not done automatically. ChimeraX tries to associate the sequences automatically but if the sequences differ enough you sometimes have to do it manually.
sir how to reduce surface on protein,we are doing docking results analysis,the protein cover the whole ligand,I am not able to saw the ligand in pocket,I have to reduce the protein bulk so clearly visualize the ligand,if you made one video on it,it would be great help professor. Kind regards Kavita
Best to ask on the ChimeraX mailing list chimerax-users@cgl.ucsf.edu. You probably want to show just the protein side-chains near the ligand to get the clearest views. Another method would be to use clip planes.
@@ucsfchimerax8387 sir you make a video on that please,thankyou for kind reply,I need less surface of protein around ligand when analyse result of docking.on transparency option also does not work for me because protein is so bulky and ligand is not visible through the bulk sir,please help. Kind regards, Kavita
The "alphafold contacts" command always colors the pseudobonds it displays between CA atoms. They might all appear to be the same color if the PAE values for all of them are nearly the same. There is another ChimeraX command "contacts" that finds close atoms but does not use PAE.
Hi. Thank you for this great tutorial. I'm newbie in protein research. I have been using Alphafold with Chimerax interface for a while. I wonder how to do docking of two different proteins that I downloaded from UniProt to see which part of those proteins interact each other? Is this tutorial also about docking? or just about protein-protein binding? Because I need to learn which part of two proteins interact each other. I'm looking forward to see answers for that. Thanks!
You can have alphafold predict a complex of 2 or more proteins by pasting their sequences into the ChimeraX AlphaFold sequence pane separated by commas. This video shows an example ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-6lXeCPuTePs.html
@@ucsfchimerax8387 what if we cannot download both sequences at the same time? I have both proteins already downloaded separately, but my computer is not powerful enough to download both of them at the same time like your video. Is there another way to simulate and find the place where these two proteins interact?
@@alonsovilca7013 If AlphaFold fails predicting the structure for two sequences that is probably because it is using old Google Colab GPUs that have limited memory (12-16 GB) and can only predict a structure of about 1200 amino acids. If you want to predict a larger structure you will need to setup AlphaFold yourself which is a good bit of work, and you will need a Linux machine with a GPU with more memory.
I'm running ChimeraX version 1.5 (2022-11-24), but it launches alphafold21_predict_colab.ipynb as in your other video ("Running AlphaFold to Predict Protein Complexes from ChimeraX") and not colabfold_predict.ipynb as shown here.. do you know how to change this? thanks!
All versions of ChimeraX use the same version of ColabFold. The alphafold21_predict_colab.ipynb notebook that runs the calculation on Google Colab is identical to colabfold_predict.ipynb. Also ChimeraX fetches this script from GitHub for each prediction which allows me to periodically update the script to newer AlphaFold / ColabFold versions. In the next few months I will hopefully be updating to ColabFold that uses AlphaFold 2.3 which is more memory efficient allowing larger structures to be predicted.
