Hi Elaine, Thank you very much for the kind reply and useful suggestions. I’ll look into these links and play with the program. Thanks, Yifan
On Jan 13, 2020, at 3:03 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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Hi Yifan, The ligand and ions will not be included in the morph trajectory model unless they are in both of the two input structures. However, you can display any of atoms from any of the input model(s) at the same time as the morph, as long as it is OK with you that these atoms do not move. See in the Models panel on the lower right of your second screenshot that the checkboxes under the “eye” icon are turned off for your two input models. You can check the box to re-show either or both of those models. You would probably want to hide the cartoon of that model, and most of its atoms except the ligand and ions.
Here are the rules for which atoms from the input structures get included in the morph trajectory, in case you want to do anything fancier to get them included so that they move along with the protein parts. See “Atoms in Common”: <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fmorph.html%23pairing&data=02%7C01%7Cyifan.wang%40utsa.edu%7C86fc3e50a84c4c34ec0108d7986c0d58%7C3a228dfbc64744cb88357b20617fc906%7C0%7C0%7C637145462181288192&sdata=Z7JoXIAeBbl2yTNW%2Fz6TwWlyh0mOumIgbyvAr5HTNhw%3D&reserved=0>
Also you may not want to show the ligand and ions except when the morph is at or near the same conformation as that structure. This can be scripted with ChimeraX commands. The “coordset” command can play any part of the morph trajectory, and then you can use “show" and “hide" between different coordset commands to turn ligand and ions on/off at the points where you wish. <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fcoordset.html&data=02%7C01%7Cyifan.wang%40utsa.edu%7C86fc3e50a84c4c34ec0108d7986c0d58%7C3a228dfbc64744cb88357b20617fc906%7C0%7C0%7C637145462181288192&sdata=8n8XktCLauzPXmkoEzwfakG8I41relXJOx5B4kGE8PE%3D&reserved=0>
See for example the ChimeraX “feature highlight” with a morphing movie. It includes the command scripts that were used. You can do all kinds of things like put on fancy labels, rotate the structure, etc. as shown in the movie. <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2Ffeatures.html%23morphing&data=02%7C01%7Cyifan.wang%40utsa.edu%7C86fc3e50a84c4c34ec0108d7986c0d58%7C3a228dfbc64744cb88357b20617fc906%7C0%7C0%7C637145462181288192&sdata=SaWYEruXc9xhfujJSqjLCjlXiPmHKir%2FE%2FVvZcOyDNg%3D&reserved=0>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 13, 2020, at 12:16 PM, Yifan Wang <yifan.wang@utsa.edu> wrote:
Dear chimeraX developer,
I am a graduate student from university of Texas at San Antonio. I’m trying to make a movie to compare two of my structures (resting state and substrate bound) using the function “morph”. But there is a problem, I very appreciate if you can help me figure this out.
As show in Figure 1, I have two structures superposed. The resting state (nude) contains an active site metal ion coordinated by three residues and 3 water molecules. And the substrate bound (blue) also contains a metal coordinated by the same residues, a remaining water molecule, and a new ligand as my substrate.
After I entered command “morph #1,2 frames 60”, I got the result of Figure 2. However, the active site metal ion and the water and substrate are missing. I want to show the active site changes between model 1 and 2. Model #3.1 seems keep the metal coordination bonds but I can’t make it present even with “show”. So my question is how to show the metal and the corresponding ligands in morph?
Regards, Yifan Wang
<Figure 1.png> <Figure 2.png>