Colouring a morph anim
Hi Team, I am seeking advice on the most effective way to visualize a morphing trajectory within ChimeraX. Specifically, I have a multi-chain model transitioning (morphing) from its starting state to its final state, and I would like to know if there is a method in ChimeraX to apply a color gradient along this trajectory. Additionally, I would greatly appreciate guidance on how to color specific atoms, such as Cα atoms, based on their overall displacement. Ideally, the color intensity (hue) would increase in proportion to the magnitude of the displacement. Best regards, Pranav Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
Hi Pranav, Easier question first: coloring by "displacement," in this case CA-CA distance between paired residues when two proteins are superimposed. Basically you would display a sequence alignment of the two proteins with the RMSD (CA-CA distance for 2 proteins) histogram shown above it, which would assign the corresponding values to the protein residues for coloring. See instructions in this previous post: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> For your other question, sorry, I don't think there is any way to gradually change color arbitrarily along the morph trajectory. The team is working on an Animation tool, but it doesn't yet do color interpolation. For coloring by RMSD specifically, I thought it might work to use "perframe" to do the RMSD coloring (as in your first question) at each step of the morphing trajectory. However, I could not get it to work; even though the RMSD histogram on the sequence alignment was changing, the coloring stayed the same through the whole morph. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 15, 2025, at 4:52 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team,
I am seeking advice on the most effective way to visualize a morphing trajectory within ChimeraX.
Specifically, I have a multi-chain model transitioning (morphing) from its starting state to its final state, and I would like to know if there is a method in ChimeraX to apply a color gradient along this trajectory.
Additionally, I would greatly appreciate guidance on how to color specific atoms, such as Cα atoms, based on their overall displacement. Ideally, the color intensity (hue) would increase in proportion to the magnitude of the displacement.
Best regards, Pranav
Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
On Nov 16, 2025, at 8:32 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
For coloring by RMSD specifically, I thought it might work to use "perframe" to do the RMSD coloring (as in your first question) at each step of the morphing trajectory. However, I could not get it to work; even though the RMSD histogram on the sequence alignment was changing, the coloring stayed the same through the whole morph.
Got this to work, with help from a colleague. Here is an example: open 2gbp open 2fw0 mm #2 to #1 show true color byattribute seq_rmsd #2 palette bluered range 0,10 morph #1,2 sequence disassociate #2/A perframe "color byattribute seq_rmsd #3 palette bluered range 0,10"; coordset #3 1,51; wait 51; ~perframe ...where the last long set of commands starting with perframe should be all one line... Also, this is just an example; if you were doing this, you might want to use a different coloring palette or a different range of values. Elaine
participants (2)
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Elaine Meng -
Pranav Shah