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UCSF ChimeraX
เข้าร่วมเมื่อ 5 มี.ค. 2021
How to use ChimeraX molecular visualization software.
Color a protein by C-alpha RMSD using ChimeraX
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.
มุมมอง: 6 481
วีดีโอ
How to predict a large protein structure with AlphaFold using ChimeraX
มุมมอง 9Kปีที่แล้ว
To predict a large protein complex (more than 1200 amino acids) with AlphaFold using ChimeraX you need to use an A100 graphics processor (GPU) on Google Colab. This video shows you how to choose the A100 GPU with 40 GB of memory. You will only be able to use the A100 GPU if you pay Google for "compute units" on Google Colab.
Color protein conformations using ChimeraX
มุมมอง 3.4Kปีที่แล้ว
I show how to color a homo-octamer protein complex to highlight where the 8 proteins differ in shape using ChimeraX 1.5.
Faster AlphaFold protein structure predictions using ColabFold
มุมมอง 26K2 ปีที่แล้ว
ChimeraX now uses an optimized version of AlphaFold called ColabFold to prediction protein structures that takes tens of minutes instead of hours. This video shows how to predict structures with ColabFold in ChimeraX.
Evaluating AlphaFold protein-protein binding with ChimeraX
มุมมอง 21K2 ปีที่แล้ว
We show how to display AlphaFold predicted aligned error for residues at the binding interface between two proteins, encapsulin and ferritin, using ChimeraX. Requires a ChimeraX daily build from June 9, 2022 or newer, or ChimeraX 1.5, not in ChimeraX 1.4. More details www.rbvi.ucsf.edu/chimerax/data/alphafold-contacts-jun2022/afcontacts.html
How to show AlphaFold error estimates with ChimeraX
มุมมอง 9K2 ปีที่แล้ว
We take a look at how to show AlphaFold predicted aligned error (PAE) plots to see if domains are packed correctly, and also show how to color by AlphaFold per-residue confidence scores. The PAE plots are in ChimeraX versions from April 2022 (not in version 1.3). More details here www.rbvi.ucsf.edu/chimerax/data/pae-apr2022/pae.html
ChimeraX virtual reality demonstration modeling encapsulin and ferritin proteins
มุมมอง 1.6K2 ปีที่แล้ว
Demonstration of ChimeraX virtual reality making an atomic model of encapsulin and ferritin proteins that store nano-crystals of iron in bacteria. Presented to the NIH Virtual and Augmented Reality Scientific Interest Group on February 17, 2022 by Tom Goddard. Outline www.rbvi.ucsf.edu/chimerax/data/vr-nih-feb2022/ferritin.html
Running AlphaFold to Predict Protein Complexes from ChimeraX
มุมมอง 34K2 ปีที่แล้ว
How to predict the structure of a photoreaction center complex of 3 proteins from ChimeraX using AlphaFold-Multimer. Requires a ChimeraX daily build newer than December 2, 2021 or version 1.4. It is not in ChimeraX version 1.3. Web page describing steps www.rbvi.ucsf.edu/chimerax/data/alphafold-dec2021/af_multimer.html
Run AlphaFold in ChimeraX for cryoEM model building
มุมมอง 5K2 ปีที่แล้ว
We show how to run AlphaFold from ChimeraX to predict a protein structure from its sequence to produce an initial model for building into a 3 Angstrom resolution cryoEM map. We look at a protein that transports omega-3 fatty acids across the blood-brain barrier, EMDB 23883. Requires ChimeraX 1.3 or a daily build newer than September 2021.
Fit an AlphaFold database model to a cryoEM map
มุมมอง 7K2 ปีที่แล้ว
We show how to start building an atomic model into a cryoEM map using an atomic structure from the AlphaFold database. We fit the atomic model into the map and adjust the position of one of its domains. The map is EMDB 30495 and is of a human dimer originally thought to be an mechano-sensitive ion channel, although the Nature publication speculates it is instead involved in lipid metabolism.
Assembling AlphaFold protein models with ChimeraX
มุมมอง 4.1K2 ปีที่แล้ว
We combine two AlphaFold protein structure predictions into an assembly using ChimeraX and find that its conformation does not match the experimental structure because the proteins are flexible. Requires September 2021 ChimeraX of newer.
Predict a protein structure using AlphaFold within ChimeraX
มุมมอง 23K2 ปีที่แล้ว
We run AlphaFold to predict the structure of the protein avidin (from chicken). We start the computation using ChimeraX (Sept 2021 version) which runs it on Google Colab servers.
Compare AlphaFold and Experimental Protein Structures in ChimeraX
มุมมอง 7K2 ปีที่แล้ว
How to fetch a predicted protein structure from the AlphaFold database and compare it to an experimentally determined structure using the ChimeraX visualization software.
Fitting an atomic model in an electron microscopy map with ChimeraX
มุมมอง 10K3 ปีที่แล้ว
I show how to make an atomic model of a nanocage by fitting an x-ray structure into an electron microscopy map and applying symmetry using ChimeraX.
How to color a protein by electrostatic potential with ChimeraX
มุมมอง 11K3 ปีที่แล้ว
Shows three ways to color nuclear export protein CRM1 by electrostatic potential using ChimeraX. More details at www.rbvi.ucsf.edu/chimerax/data/electrostatics-apr2021/crm1.html
Color a cryoEM Map by Local Resolution using ChimeraX
มุมมอง 8K3 ปีที่แล้ว
Color a cryoEM Map by Local Resolution 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".
if you are multimer the file should be "scores_rank_001_alphafold2_multimer_v3_model_4_seed_000.json"
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?
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".
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.
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!
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.
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.
This is really great. For homomeric proteins, i,.e., a homodimer, do you copy the amino acid sequence twice separated by a coma?
Yes
Thank you so much!
Thanks for the video! I cannot access the header Ca RMSD when I right click on the sequence, any idea why?
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
Please ask on the ChimeraX mailing list. Your question is not related to the content of this video.
When I use the contacts command it doesn't colour the contacts by PAE, how can I change that?
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.
Thank you so much for this nice tutorial
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 th-cam.com/video/6lXeCPuTePs/w-d-xo.html
@@ucsfchimerax8387 Thank you for this quick reply!
@@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.
Thanks a lot for the useful tool and great tutorials. I have two predicted structures and am trying to compare them. When I use AlphaFold Coloring Function, do not get any results with the missing structure, c-alpha distance greater than, etc. Could you please guide me with the issue? P.S. I use November 2022 version. The daily version doesn't work at all, and gives a blank layout when the software is launched.
The ChimeraX AlphaFold Coloring panel only compares a predicted structure to another structure that was used to provide the sequence for the prediction (e.g. an experimental structure). It would be useful if it could compare any two aligned structures, but it doesn't. Here is the AlphaFold Coloring documentation www.cgl.ucsf.edu/chimerax/docs/user/tools/alphafold.html#coloring
Hi, can you please help me with modified sequence predictions? like I have a protein that has an acetyl group, how to input that in the sequence to predict hetero dimeric structure?
AlphaFold only predicts structures containing the 20 standard amino acids.
How would you then add the 2nd copy of the alphafold protein in the cryoEM dimer? Simply repeat the steps, but for the other monomer?
Yes repeat the steps to fit the second monomer in the cryoEM map. Or you could instead run a prediction of the dimer by pasting both sequences into the ChimeraX AlphaFold panel separated by a comma. The prediction can take about 30 minutes.
@@ucsfchimerax8387Thank you, just seeing this now!