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{"@context":"https://schema.org","@type":"DiscussionForumPosting","headline":"Cannot Determine Side Chain Positions from Backbone Only","articleBody":"### Description:\nThe current implementation of **DiffPack does not allow for the determination of side chain atom positions** starting from a backbone structure **if no initial coordinates for the side chain atoms are provided.**\n\n### Expected Behavior:\nIt should be possible to generate or predict reasonable side chain conformations based solely on the backbone coordinates, even when initial side chain atom positions are missing.\n\n### Actual Behavior:\nIf the input structure contains only backbone atoms (N, CA, C, O), foo cannot generate or assign positions for the side chain atoms. This limits its usefulness for building or refining protein models from backbone-only data.\n\n### Steps to Reproduce:\n\n    Provide a PDB file with only backbone atoms for a polypeptide chain.\n\n    Run DiffPack to attempt to generate the full structure.\n\n    Observe that side chain atoms are missing or not positioned.\n\n**Environment**:\n\n   config file is attached in the current issue\n\n[log.txt](https://github.com/user-attachments/files/20638021/log.txt)\n\n### Additional comment:\nthis limitation seems to be unaddressed in both the paper and the documentation, and it greatly restricts the software’s scope of application in scenarios where only backbone coordinates are available.","author":{"url":"https://github.com/dallouche","@type":"Person","name":"dallouche"},"datePublished":"2025-06-07T09:34:23.000Z","interactionStatistic":{"@type":"InteractionCounter","interactionType":"https://schema.org/CommentAction","userInteractionCount":1},"url":"https://github.com/12/DiffPack/issues/12"}