Thanks Elaine. I'm still unclear on how to make a movie where I move from solid to mesh to mesh w/ crystal structures. Should I save each form (i.e solid, mesh, etc.) individually and then use a morph command to progress through each one? (If this is the case could you give me an example command line I could refer to?) Or would this involve setting all of the models up via command lines as the movie was recording? I sincerely appreciate your infinite patience with me and my questions. Desiree ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Tuesday, November 20, 2012 1:42 PM To: Benefield, Desiree A. Cc: Chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Movie with multiple models Forgot to mention, you would probably want to figure out the desired contour levels using the sliders on the histogram in the Volume Viewer GUI first. Then you can put those settings in your command script. Elaine On Nov 20, 2012, at 11:40 AM, Elaine Meng wrote:

Hi Desiree, We understand it can take a while to get up to speed -- Chimera has a lot of stuff in it!

You can use the volume command to change the display style of the map (also contour levels, colors ...), e.g.:

vol #0 style mesh level 20 color goldenrod

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html>

You could use the modeldisplay and ~modeldisplay commands to show/hide the crystal structures. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/modeldisplay.html>

Chimera command index: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>

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

On Nov 20, 2012, at 10:59 AM, Benefield, Desiree A. wrote:

...

Hello again,

I have a 3D reconstruction volume file. I'd like to show the initial model as a solid surface, then as a mesh surface, and then as the mesh surface with crystal structures. Can you recommend the best way to approach this? Specifically, I am uncertain as to what command will help me accomplish this and/or if I need different chimera files for each form of the model...

Very sorry to keep bothering you. I appreciate the advice.

Desiree

Thank you Elaine. I sincerely appreciate your help. I will explore your suggestions further. Thanks for your time and have a nice Thanksgiving! Desiree ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Tuesday, November 20, 2012 3:37 PM To: Benefield, Desiree A. Cc: Chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Movie with multiple models Hi Desiree, I'm not totally clear on what you are trying to do. Morphing is only for changing the shape of something, not whether or how it is displayed. You would use morphing to show the difference between maps from different experimental conditions, or between different conformations of an atomic structure. General information on making movies: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html> With the volume command you can change from solid to mesh and with modeldisplay command you can hide and show models, including maps and/or atomic structures. Those things happen abruptly, however. If you just mean you want to fade in and fade out things gradually over several frames, it can be done with the movie command crossfade option, but only if nothing is being moved during the crossfade. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html> If there are movements (position changes) occurring concurrent with the display changes in your desired movie, you could try using the new Animation interface (you would need to get Chimera version 1.7, i.e. a recent daily build). You would save "scenes" and then arrange them on a timeline, and then Animation would take care of gradually transitioning from one to another. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/animation/animation.html> Daily build download: <http://www.cgl.ucsf.edu/chimera/download.html#daily> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Nov 20, 2012, at 12:29 PM, Benefield, Desiree A. wrote:

Thanks Elaine. I'm still unclear on how to make a movie where I move from solid to mesh to mesh w/ crystal structures. Should I save each form (i.e solid, mesh, etc.) individually and then use a morph command to progress through each one? (If this is the case could you give me an example command line I could refer to?) Or would this involve setting all of the models up via command lines as the movie was recording? I sincerely appreciate your infinite patience with me and my questions. Desiree