Hi Leonardo, I tested the new daily build, version 1.9.dev202407052353 (2024-07-05), and it works to show the molecular surface colored by Coulombic electrostatic potential (ESP) for each frame in a morph trajectory. First I set up my example. I open two structures (models #1 and #2), superimpose them, and then morph them to create a morph trajectory (model #3) with 51 frames. Example setup commands: open 2gbp open 2fw0 mm #2 to #1 morph #1,2 Morphing only morphs the positions of the atoms. It doesn't matter if you had shown surfaces for the input structures. After you have created the atomic morph trajectory, then you need to play it back with the "coordset" command, using the "perframe" command to perform other actions at each frame of the trajectory, namely showing a molecular surface colored by Coulombic ESP. The following command should be all one one line in which different commands are separated by semicolons. The email display program may break it into multiple lines, but it should all be entered as one line into the ChimeraX command line, and the quotation marks should be the simple plain text ones from the keyboard, not fancy/curly ones (some mail programs also change those!!): perframe "coordset #3 $1 ; surf close ; surf #3 update false ; coulombic surf #3" range 1,51 My example is with morph trajectory model #3 that has 51 frames in it. You would need to revise the above if your morph trajectory model number is different or it has a different number of frames in it. Of course, you have to download and use the new daily build, because older versions will have the bug that prevents the above from working. See the help pages of the various commands for details on their options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coulombic.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#options> This answer is in analogy to a previous post to chimerax-users in which the same thing was done, except to show the MLP (lipophilic potential) instead of ESP: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax- users@cgl.ucsf.edu/message/SZLHTVU6MEEWRIJA44IM5AZGRIDQMD2O/> 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 Jul 5, 2024, at 1:32 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Leonardo, The morphing is only on the atomic positions, so it doesn't matter whether or not you calculated or colored molecular surfaces on the starting structures.
Instead you would first create the morph trajectory model (of atomic positions) and then replay it, showing and coloring the surface for each frame of the morph trajectory during playback. This process involves using the "coordset" command to play the trajectory and the "perframe" command to apply other commands to each frame. This currently works fine for "mlp" as described in the last two commands in this previous chimerax-users post:
<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...>
However, my testing of the same approach for "coulombic" revealed some bugs that prevent it from working correctly. A fix has been applied to the code but is not yet available in the daily build. I will get back to you next week after I can test the future daily build to make sure it works.
Talk to you later, 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 Jul 4, 2024, at 3:46 PM, Leonardo Talachia Rosa via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX community, I hope you are well. I have a set of models for which I want to show the exposure of specific regions as protein changes conformation through morphing. I can do a morphing between atoms or ribbons, and that looks ok, but the presentation would benefit from a morphing between surface representation coloured by electrostatic potential of each state. I scavenged the youtube tutorials and chimeraX documentation but could not find a way to do it. Would anyone know how to produce this? All models have identical sequence and I calculated the surface for all of them. Thank you for your time, Kind wishes, Leonardo