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?
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, I have a question. I recently identified some candidate sequences from different species that I suspect them to be member of enzyme family A. I produced structural models of these candidates by AlphaFold. There is only one experimentally determined structure of enzyme A from yet another organism. I would like to make a comperative analysis using ChimeraX to claim that my candidates are genuine enzyme A. I don't know how to do that by ChimeraX to produce a publishable analysis? Could you please make a comment on this?
@@danclayton5996 Hi! Sorry not to explain in the first place. I opened two model. From Tools menu, select structural analysis and match maker. From the pop-up window select reference structure and structure to match. That's it! I hope it helps!
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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?
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,
I have a question. I recently identified some candidate sequences from different species that I suspect them to be member of enzyme family A. I produced structural models of these candidates by AlphaFold. There is only one experimentally determined structure of enzyme A from yet another organism. I would like to make a comperative analysis using ChimeraX to claim that my candidates are genuine enzyme A. I don't know how to do that by ChimeraX to produce a publishable analysis? Could you please make a comment on this?
Hi, Did you figure out how to do this yet?
@@danclayton5996 Yeah I did.
@@yonetmen Care to explain how? If you have time..
@@danclayton5996 Hi! Sorry not to explain in the first place.
I opened two model. From Tools menu, select structural analysis and match maker. From the pop-up window select reference structure and structure to match. That's it! I hope it helps!
@@yonetmen Thanks!!