Question received during the C4 tutorial

Here is a partial list of the questions you raised during the tutorial. The ones in red have an answer.

How to add traces to selected moving atoms in VMD?

At the first frame store each selected atom position. Then at each frame draw a line from the stored position to the current one and update the previous position.

How to combine volumetric cubes to show differences in density?

In STM4 provide a simple interface for "data math" module.

How to make searches on the VMD mailing list?

The entire vmd-l mailing list archive is online, and the full-text searches are only on the entire VMD site. Gmane seems do not cover vmd-l list.

In VMD I need a chart of some scalar quantity varying over a trajectory

Nice idea for a plugin! A plugin with picking capabilities to move to the requested step and vice versa. I need to find a charting component for Tcl/Tk.

How to force VMD to recompute bonds every timestep?

mol bondsrecalc <molid>

How to change colormap in VMD?

I have to check.

Suggestions for standard formats for volumetric data

Gaussian cube is tied to Gaussian. Molden format seems a good compromise. Q5cost is OK, but not yet used.

Could you make available the mencoder frontend?

Sure! It is called mefe.

Not a question: Gabedit could be an interesting free modeler

Installed, tested and added to my tool pages.

How to draw arrows in VMD?

Look at the VMD manual page for draw; it has an example.

I have to visualize thousand of glyphs on the screen and my GTK-X11 application goes out of memory.

Try to switch to OpenGL based widgets either inside GTK or with WxWidgets.