<p>I am using <code>VMD</code> to visualise the secondary structure of protein <a href="https://www.ks.uiuc.edu/Research/vmd/" rel="nofollow noreferrer">here</a>.</p>
<p>The trajectories are from my Gromacs simulation. Firstly I use <code>File - New Molecule...</code> to load the <code>protein.gro</code> file. Secondly I use <code>File - Load Data into Molecule...</code> to load my <code>protein.xtc</code> trajectories.</p>
<p>Then I use <code>Cartoon</code> to visulise the structure. As I drag the time frames, all the secondary structures (e.g. alpha-helix, beta-sheet) stay the same. But I am pretty sure some of them are changing, as I look into the <code>Timeline</code> analysis for secondary structure.</p>
<p>So</p>
<ol>
<li>how do I use <code>VMD</code> to see the secondary structures at different time frames?</li>
<li>Is there an alternative software that can do this?</li>
</ol>

CC BY-SA 4.0
2020-12-07T02:55:53.303Z
Try here: https://mattermodeling.stackexchange.com/. There's way more VMD questions there.
user1271772
CC BY-SA 4.0
2020-12-07T15:35:03.393Z
Can I move my questions there?
lanselibai
CC BY-SA 4.0
2020-12-07T16:00:44.763Z
copy and paste them.
user1271772
CC BY-SA 4.0
2021-07-04T04:53:57.100Z
I’m voting to close this question because it seems to be a better fit for another community.
gringer
<proteins><protein-structure><visualization>
Can VMD change its cartoon representation for secondary structure according to trajectories?
# Can VMD change its cartoon representation for secondary structure according to trajectories?

(Asked by: username_0 on 2018-01-30)

I am using `VMD` to visualise the secondary structure of protein [here](https://www.ks.uiuc.edu/Research/vmd/).

The trajectories are from my Gromacs simulation. Firstly I use `File - New Molecule...` to load the `protein.gro` file. Secondly I use `File - Load Data into Molecule...` to load my `protein.xtc` trajectories.

Then I use `Cartoon` to visulise the structure. As I drag the time frames, all the secondary structures (e.g. alpha-helix, beta-sheet) stay the same. But I am pretty sure some of them are changing, as I look into the `Timeline` analysis for secondary structure.

So

1. how do I use `VMD` to see the secondary structures at different time frames?
2. Is there an alternative software that can do this?

**Tags:** proteins, protein-structure, visualization
> **Comments:**
> **username_1**: Try here: https://mattermodeling.stackexchange.com/. There's way more VMD questions there.  
> **username_0**: Can I move my questions there?  
> **username_1**: copy and paste them.  
> **username_2**: I’m voting to close this question because it seems to be a better fit for another community.  

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## 0 answers

