Zhanglab forum

The results of DMFold job for DMF042779492 have been received. Thank you very much. May I ask how to view the interaction sites between the two proteins in the results? I just got the three-dimensional structures of the two proteins. Are there any corresponding video tutorials?

Dear anhuifei,

Thank you for using DMFold, and we’re glad to hear that you’ve received the predicted structure for your job DMF042779492.

To view the interaction sites between the two proteins, we suggest the following steps:

1. Visualize the Complex in PyMOL
The predicted complex structure file (usually in PDB format) can be loaded into PyMOL. You can use the following commands to highlight the interface region:

load DMF042779492.pdb
show cartoon
color blue, chain A
color red, chain B
select interface, (chain A within 5 of chain B)
show sticks, interface

This will highlight residues of Chain A that are within 5 Å of Chain B (and vice versa).

2. Use Interface Analysis Tools

If you prefer automated analysis, you can upload the structure to tools such as PDBePISA or ProteinsPlus InteractiVenn to obtain residue-level interaction details including hydrogen bonds, salt bridges, and hydrophobic contacts.

3. Video Tutorials
While we are still in the process of preparing video tutorials for DMFold, you may find general PyMOL tutorials helpful. Here are two recommended resources:
• PyMOL Basics
• YouTube: Protein Interface Visualization

If you need further assistance or would like us to highlight the interface residues for you, feel free to upload your PDB file or share specific requirements.

Best regards,
ITASSERteam

Use PyMOL or Chimera to open two protein structures, then view contact areas by looking for amino acid pairs that are less than 5Å apart. You can use the distance command in PyMOL or the Contacts command in Chimera to identify interaction areas.

You now have a 3D structure from DMFold – the next step is to use PyMOL (or Chimera) to view and highlight the interaction regions between the two proteins. The select interface command will help you quickly identify residues that are in close contact. If you wish, you can utilize real analysis tools to examine the details of each interaction.

Lillian Quinn wrote: ↑Tue Jun 24, 2025 10:29 am Use PyMOL or Chimera to open two protein structures, then view contact areas by looking for amino acid pairs that are less than 5Å apart. You can use the distance command in PyMOL or the Contacts command in Chimera to identify interaction areas. wordle unlimited

It's live style

Has anyone tried combining DMFold results with PDBePISA or another interface-analysis tool to automatically list all hydrogen bonds/salt bridges at the interface? I’m curious if that gives a clearer picture than just the 5 Å selection in PyMOL.