Body: <p>I'm currently working on a secondary structure prediction model and I'd like to visualize what will be predicted , the format of secondary structure sequence is consisted of 8 labels:</p>
  <ul>
  <li>G: 3-turn helix (310 helix)</li>
  <li>H: 4-turn helix (α helix)</li>
  <li>I: 5-turn helix (π helix)</li>
  <li>E: Extended strand in parallel and/or anti-parallel β-sheet conformation</li>
  <li>T: Hydrogen bonded turn (3, 4 or 5 turn)</li>
  <li>S: Bend (includes β-turns)</li>
  <li>B: Bridge (includes disulfide bridges)</li>
  <li>C: Coil (includes irregular and random coil regions)</li>
  </ul>
  <p>Example from the dataset:</p>
  <pre><code>BPPHHHHHHHHHHTT TTBTTB HHHHHHHHHHHHTTBTT EEEETTTTEEEETTTTEETTTT B SS 
  SS   TTS BGGGGGSSS HHHHHHHHHHTTSTTGGGGSHHHHHHTTTS  GGGTTTS
  </code></pre>
  <p>The output of the prediction should be a string similar to the example I show above.</p>
  <p>Are there any libraries that could help me with automatized visualization of protein secondary structure? Can I do it in python and than use the visualization on the web? Or can I create it directly on the web? I don't have to write the visualization from scratch. I tried to google stuff, but got practically no answers, just examples of similar visualization by other programs (e.g. 2Dprots).</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-07-11T14:44:56.430Z
Comments.Text: Please [edit] your question and clarify. All you have told us is that you are working on secondary structure. What format are your files in? Can you show an example? What do you want to visualize exactly? Al[ha helices, beta sheets, that kind of thing? Regions of disorder? Do you need to write your own or can you use an existing one? When you searched for "visualize protein structure" with your favorite search engine, did none of the results work for you? Why? What do they lack?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-07-17T23:05:41.553Z
Comments.Text: So it seems like you are intending to do something very similar to [DSSP](https://github.com/PDB-REDO/dssp/blob/trunk/doc/mkdssp.md). What I don't understand is whether you are actually writing a prediction tool or if you just want a tool like DSSP to write these labels, which are I believe exactly the same as what you are using. It doesn't seem that you want an actual structure visualizer like PyMol?
Comments.UserDisplayName: Maximilian Press
Tags: <python><protein-structure><visualization><secondary-structure>
Title: How can I visualize protein secondary structure?
ThreadText: # How can I visualize protein secondary structure?
  
  (Asked by: username_0 on 2024-07-11)
  
  I'm currently working on a secondary structure prediction model and I'd like to visualize what will be predicted , the format of secondary structure sequence is consisted of 8 labels:
  
  * G: 3-turn helix (310 helix)
  * H: 4-turn helix (α helix)
  * I: 5-turn helix (π helix)
  * E: Extended strand in parallel and/or anti-parallel β-sheet conformation
  * T: Hydrogen bonded turn (3, 4 or 5 turn)
  * S: Bend (includes β-turns)
  * B: Bridge (includes disulfide bridges)
  * C: Coil (includes irregular and random coil regions)
  
  Example from the dataset:
  
  ```
  BPPHHHHHHHHHHTT TTBTTB HHHHHHHHHHHHTTBTT EEEETTTTEEEETTTTEETTTT B SS 
  SS   TTS BGGGGGSSS HHHHHHHHHHTTSTTGGGGSHHHHHHTTTS  GGGTTTS
  
  ```
  
  The output of the prediction should be a string similar to the example I show above.
  
  Are there any libraries that could help me with automatized visualization of protein secondary structure? Can I do it in python and than use the visualization on the web? Or can I create it directly on the web? I don't have to write the visualization from scratch. I tried to google stuff, but got practically no answers, just examples of similar visualization by other programs (e.g. 2Dprots).
  
  **Tags:** python, protein-structure, visualization, secondary-structure
  
  > **Comments:**
  > **username_1**: Please [edit] your question and clarify. All you have told us is that you are working on secondary structure. What format are your files in? Can you show an example? What do you want to visualize exactly? Al[ha helices, beta sheets, that kind of thing? Regions of disorder? Do you need to write your own or can you use an existing one? When you searched for "visualize protein structure" with your favorite search engine, did none of the results work for you? Why? What do they lack?  
  > **username_2**: So it seems like you are intending to do something very similar to [DSSP](https://github.com/PDB-REDO/dssp/blob/trunk/doc/mkdssp.md). What I don't understand is whether you are actually writing a prediction tool or if you just want a tool like DSSP to write these labels, which are I believe exactly the same as what you are using. It doesn't seem that you want an actual structure visualizer like PyMol?  
  
  ---
  
  ## 0 answers
  
  