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Can VMD change its cartoon representation for secondary structure according to trajectories?

Can VMD change its cartoon representation for secondary structure according to trajectories?



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I am usingVMDto visualise the secondary structure of protein.

The trajectories are from my Gromacs simulation. Firstly I useFile - New Molecule…to load theprotein.grofile. Secondly I useFile - Load Data into Molecule…to load myprotein.xtctrajectories.

Then I useCartoonto visulise the structure. As I drag the time frames, all the secondary structures (e.g. alpha-helix, beta-sheet) keep the same. But I am pretty sure some of them are changing, as I look into theTimelineanalysis for secondary structure.

So how to useVMDto see the secondary structures at different time frames?

Thanks a lot for @Stefan's help! It finally works! So follow Stefan's guide, and replace themolidwith the number under theIDin theVMD Main.


As Martin pointed out, VMD doesn't update secondary structure content over the course of an MD trajectory. You can easily do this in VMD by using the SSCache script:

http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/sscache/sscache.tcl

I believe it ships with the newest versions of VMD, actually, but I'm not exactly sure; even if not, you can easily source it:

Extensions > Tk console (in the console, typesource Downloads/sscache.tcl(or where ever you've saved the script)). Once you've sourced the script, the easiest thing to do would be to load your topology and trajectory and (in the Tk console) issue the commandstart_sscache molid, although I advise having a look at the examples and options in the script.


Animating the secondary structure in VMD

The secondary structure definitions for the molecules in VMD don't change during an animation but they can be made to do so with a trace on the vmd_frame($molecule) Tcl variable. The simplest way is to call vmd_calculate_structure(molecule) every time the frame changes…


Watch the video: VMD 162A Final: Alvin Wu (August 2022).