[Chimera-users] Saving files from MD Movie

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 5 09:51:30 PST 2019

Hello Maja,
The “save PDB” dialog is the same whether you open it from the main menu or the MD Movie menu.  For trajectories such as from morphing, it includes an option to save “current frame” or “all frames” … you’d need to choose the latter.  That will save all the frames as multiple MODEL sections in one PDB file (as is used for NMR ensembles in the Protein DataBank).  This is a normal/standard format, but I don’t know how Maya interprets it.

However, if you need multiple individual PDB files, you can get that with a couple more steps. If you reopen that saved single PDB file in Chimera, it displays all the frames at once, but they are opened as separate models and can be hidden/shown etc. independently.  I.e. in the Model Panel after reopening the file it will be listed as one combined item but if you choose “group/ungroup” on the right side of the Model Panel, that will expand to list each one #0.1, #0.2, ….. #0.N

Now since it is opened as multiple models instead of a trajectory, if you choose “save PDB” from the File menu, there is a choice to save multiple models in a single file or multiple files.  Choose the latter. (Keep all of the models chosen in that dialog, i.e. do not do this individually one model at a time.)  Then you literally have to enter a name that includes $name or $number so that the single name can be expanded appropriately into multiple names.  For example, if you enter filename “junk$number.pdb” you would get junk0.1.pdb, junk0.2.pdb, …. junk0.N.pdb with model numbers embedded in the generated names.

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

> On Mar 5, 2019, at 2:05 AM, Divjak Maja <Maja.Divjak at petermac.org> wrote:
> Hello! 
> I have been using Chimera for analysis of H-Ras morphing from its GDP-bound inactive state to the GTP-bound active state. It works very nicely and a lovely movie is produced. What I am having difficulty with however, is saving the output of the morph as a series of PDB files that I can import to Autodesk Maya with the molecular Maya plugin. When I try to save from the movie window ie using file >save PDB, all I get is one PDB file containing a single structure. I also tried to save using the main window file > save PDB > save all frames and the same thing happens. I then tried selecting each frame individually and saving with unique numbered file names, but again, when trying to import into Maya, all I get is one structure, not a changing structure. Even the first and last frame PDBs are the same. Could you please advise as to how to save the morph output as a useful PDB series, I must be missing something? 
> Thanks so much and best wishes, 
> Maja

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