I have iPyMOL and have put eMovie_rigimol.inp in the main PyMOL directory but the morphing does not work through eMovie. (I get the error : 'FILE-ERR: unable to open file eMovie_rigimol.inp') - How can I solve the problem?

When you create a morph, you need the file eMovie_rigimol.inp to be in your current working directory. A good idea is to put eMovie_rigimol.inp into /ipymol/ the main PyMOL directory NOT ipymol/modules/pmg_tk/startup) because usually when iPyMOL starts, this is the default working directory. If you've navigated away (in iPyMOL) from the directory that contains eMovie_rigimol.inp, you can check/change the current working directory of your open iPyMOL program by using the typed command window of iPyMOL ('iPyMOL Tcl/Tk GUI').

How do I cite eMovie?

If you use eMovie to create a movie or animation for a presentation, website, supplementary material for a paper, or for any other purpose, please cite eMovie. Please cite eMovie like this:

Movie made using eMovie.
Hodis, E., Schreiber, G., Rother, K., Sussman, J.L., eMovie: a storyboard-based tool for making molecular movies, Trends in Biochemical Sciences 32, 199-204 (2007).

Please don't forget to cite PyMOL as well.

How can I make it so that eMovie does not start when I open PyMOL, but rather only starts when I select it from the PyMOL GUI Plugin drop-down menu?

In the file eMovie.py, which you should open using a text-editor, you can comment out one line so that eMovie does not open automatically when PyMOL starts. That line in its entirety reads "open_eMovie()" (and in eMovie v1.04 should be on line 191). To comment out this line, add a "#" to the beginning of the line so that the entire line now reads "#open_eMovie()". Save eMovie.py and exit. If you would at any point like to revert to eMovie opening automatically upon PyMOL launch, just go back and remove the "#" that you have added.

When I make a morph, the secondary structure disappears from the morph. How can I recover the secondary structure?

To recover secondary structure after creation of the morph: In the PyMOL GUI, the new morph object, like all objects, will have the square buttons A, S, H, L, and C to the right of the object name, (for Actions, Show, Hide, Labels, Colors) in the column on the right-hand side of the PyMOL viewer where all the objects and selections are listed by name. Click on the A button next to the morph object and in teh drop down menu that appears, select "assign secondary structure". This should fix the problem. If it fails, try saving the movie using "Save eMovie" and then quit, and then load the movie using "Load eMovie".

I've made a movie, but when I try to export it with ray tracing, the first few images are exported as ray-traced frames, and then suddenly the "set ray_trace_frames=off" command is issued for apparently no reason and the rest of my frames are exported without ray-tracing.

We're not entirely sure why this happens, but it may be a memory issue. To work around it, first type "set ray_trace_frames=on" in the PyMOL command window. Next, type "mpng prefix", also in the PyMOL command window, where "prefix" is the prefix you would like to give the image files to be exported. The output files will look like this "prefix001.png", "prefix002.png", etc.

I can make a morph with eMovie using iPyMOL (incentive PyMOL), but I can't play it back in a movie.

Make sure you're using iPyMOL v0.99. This is currently the only version of iPyMOL that eMovie supports.

I have a question that hasn't been answered on this website or in the eMovie paper in TiBS, who can I ask?

Send Eran Hodis an email. His email is his first name then a period then his last name @weizmann.ac.il like this: first.last@weizmann.ac.il (We refrain from writing out the email explicitly to protect from spammers that mine the Internet for emails).

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