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Visualize ribbon diagrams of proteins

Hi,

I am performing MD simulations of fibronectin, which is a protein, in LAMMPS and  visualizing the same in Ovito. While I can visualize atoms and bonds, can I visualize the ribbon diagrams of protein molecules in Ovito? I am trying to draw a surface over backbone atoms but have not been able to generate anything similar to ribbon diagrams. Could you please suggest ways of viewing ribbon diagrams of proteins in Ovito? I have attached a lammps data file and a ribbon diagram of the same protein for your reference.

Best regards,

Sandipan

Uploaded files:

Hi Sandipan,

Thank you for your question. Displaying ribbon diagrams of protein molecules is not one of the capabilities of OVITO yet. You can find the list of visual element types currently supported by the software in our documentation.

Thus, I am afraid a cannot give you a helpful answer in this case. However, if there is enough user interest in this kind of program feature, we will try to implement it in a future version of OVITO. You are the first to explicitly ask for this visualization capability, but I can imagine that there will be more users who would benefit from such as addition.

You mentioned a ribbon diagram that you wanted to attached for reference. For some reason, I cannot see such as diagram file, only the LAMMPS data file is there. Can you please try again? Thank you.

-Alex

Hi Alexander,

I have attached the ribbon diagram of the fibronectin protein (generated in VMD). My attachment in the earlier post failed because it was in an incompatible format.

Let me take this opportunity to place a request to you to add the capability of viewing ribbon diagrams of proteins in Ovito. I hope that there will be many researchers in the Biomacromolecules community who will benefit from this.

Thank you so much for the wonderful visualization capabilities and analyses tools which are already there in Ovito.

Best regards,

Sandipan

Uploaded files:
  • fn.jpg

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