[Chimera-users] making images of the intermediate steps of morphing

[Elaine Meng]

Hi Anindito,
Chimera opens the morph as a trajectory.  If you only want to show one intermediate, then you can put the trajectory at that frame with the MD Movie GUI or "coordset" command, and then also display the original structures (the ones you used to make the morph).  You can make the trajectory a lighter or different color, and/or transparent.

That is how I made the figure shown in this the tutorial:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html#sameprot>

However, if you want to show more than one intermediate step:
Chimera does not allow simultaneously showing more than one frame of a trajectory.  To show more than one frame at a time, you have to save PDB file(s) from the trajectory, and then open the saved PDB (you could close or hide the trajectory). 

You could either save one multi-model PDB that has all the frames of the trajectory, or you could repeatedly show the frame of the trajectory that you want, and choose the option to save a single model PDB of only the currently displayed frame (i.e. you would have to change display frame, save again, for each separate single model PDB that you want).

You can save your morph trajectory to PDB using menu: File... Save PDB.  In the Save PDB dialog, choose the morph model, and then either save "current frame" to a PDB file (and then show a different frame, repeat as many times as you need), or "all frames" together with the option to "Save multiple models in a single file".  If you open a multi-model file the individual frames are submodels (e.g. if opened as #4, they will be #4.1, 4.2, 4.3 etc. and can each be treated separately for show/hide/coloring etc.).
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>

I would just use the second approach to save a single file instead of having to save multiple files, but of course do whichever seems easier to you.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 1, 2022, at 6:24 AM, Sen, Anindito via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear Chimera users,
> How can I generate an image with the intermediate steps in a morphing session (of an atomic structure between its two conformations).
> The image of intermediate states can appear 'lighter' than the original and final states.
> Stay safe & Regards
> 
> Anindito Sen. Ph.D
> 
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