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Thank you! Could you please let me know how to check the interaction between several proteins simultaneously... i.e., show all the interactions within let's say 5A in a multimeric protein complex?

Alpha fold gives me 5 models. Which model should I count as the best model for my query protein?

Thanks! Please, and how to save the new atomic model(?) with the map to elaborate the report, please if you have a template report, I will be so grateful with you.

Thank you for showing where the files were downloaded!

😊

Thanks very much Tom for the tutorial, very useful indeed, much appreciated.

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?

Do you need to add a space or new line between the commas?

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?

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

Thnak you so much for this informative tutorial.

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.

Which pallete coloring format is the "Color PAE domains" using? esmfold, alphafold, paecontacts, rainbow?

thanks, why no .dx file output in my job of PDB2PAR?

I run command "color bfactor #1 palette alphafold", but I think the color is not so good. How can I modify or redefine the palette alphafold?

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?

Absolutlely amazing. I have been using ChimeraX/AlphaFold for over a year. It has sped up research in some fields by an order of magnitude.

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 sharing.

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

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?

Once I have the contacts between structure A and B, is there the possibility to get a list of those contacts (to have a better overview)?

I want to predict my vaccine structure. Do I also put the adjuvant sequence or just the epitope protein from MHC 1 AND 2? Any response is appreciated.

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.

Does anyone know if you can use ChimeraX with Autodock Vina

Does anyone know if you can use ChimeraX with Autodock Vina

Thank you so much.

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".

How can I save it as a pdb file. I can only save it as py and ipynb, which I cannot open in chimeraX

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

Hey thanks so much for the help, quick question: what is the different between color PAE domain and color pLDDT ?

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?

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

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

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 .

I never comment, but honestly thank you so much for this! So straightforward and I was about to give up completely on alpha fold!

🎉🎉🎉

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?

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

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

Where did u get the experimental file from

Thanks for sharing!

wow, can't imagine what we could do in the next few years. amazing work.

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.