Hi Giorgio I mostly answered for volumes (maps) but if you are just showing molecular surfaces, they should just change automatically with the atoms as long as there isn’t a molecular surface calculation failure. However, as mentioned, “coordset” does not create the atomic morph, it just plays it back. To create the atomic morph before playing it back with “coordset", use: Chimera: Morph Conformations tool (there is also a “morph” command but in my opinion rather difficult to use) <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/morph.html> Chimera movie tutorial with atomic morphing example: <http://www.rbvi.ucsf.edu/chimera/data/nih-oct2012/movies.html> ChimeraX: “morph" command (improved from Chimera to be much easier to use) <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html> I hope this helps, and sorry if I misunderstood your question. Best, Elaine

On Apr 2, 2018, at 9:24 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Giorgio, In both chimera and chimerax, the command for morphing maps is different than for morphing atomic structures. You are looking at the wrong example in that page — look at the ”vop morph” example, not coordset. Coordset just plays back an atomic ensemble or morph trajectory that was already calculated, e.g. with the morph conformations tool or morph command.

For maps:

chimera command: vop morph <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#morph> chimera tool: morph map <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morphmap/morphmap.html> chimera tutorial: <http://www.rbvi.ucsf.edu/chimera/data/santa-cruz-aug2012/animate.html>

chimerax command: voume morph <http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#morph>

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Apr 2, 2018, at 8:31 AM, Giorgio Luciano <giorgio.luciano@gmail.com> wrote:

Hello ! I was looking at the script for morphing among structures that can be found here http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html (coordset #1 1,161). I've tried to use the surfacecat command in the script in order to obtain a morph through volumes since my idea was to create the movie and then export all the surface perframe in order to use them in another 3d software. I've seen that surfcat can actually create volumes for all the surfaces included in the 1r7w but morph start does not seems to work among the surface created. I've seen also that it could be a solution to create density maps from the surface and them morph them using volume viewer but it seem quite an awkard solution (at least for me that I'm no expert :) I've tried to find the limitation of morph command but it does not report anything regarding surfaces. Any help is very appreciated. Sorry for the cross-posting

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Hi John, The PDB format only supports single-character chain IDs (one of the reasons for mmCIF format), so it is impossible to save structures with more than 36 chains in PDB format without losing chain information. A semi-workaround is to: 1) In ChimeraX: split the structure into multiple structures, one per chain (“split #1”) 2) Save those models into a multi-MODEL PDB file (“save ~/rib.pdb models #1”) 3) Read them into Chimera. 4) If there are <= 36 models, combine them into a single model (“combine” button of the Model Panel), otherwise you just have to work with them as separate models. —Eric Eric Pettersen UCSF Computer Graphics Lab

On Apr 2, 2018, at 2:29 PM, John Mercer, Ph.D. <jmercer@duke.edu> wrote:

Hi Elaine,

I load a ribosome mmcif file in ChimeraX and save it at as a PDB file. It loads and works fine in Chimera but all the chain identifiers have disappeared. Is there away to save a PDB file from ChimeraX that retains the identifiers? I am wanting to use the larger set of tools in Chimera when only mmcif files are available.

Best, -John _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users