{
  "id": 575485,
  "title": "What defines the origin (0,0,0) for the protein structure?",
  "url": "/competitions/stanford-rna-3d-folding/discussion/575485",
  "author_name": "",
  "post_date": "2025-04-29T01:44:15.543097Z",
  "votes": null,
  "comment_count": 3,
  "views": 0,
  "content": "<p>I am a total beginner at this. I am unclear on what determines the origin (0,0,0) of the protein structure. I would have thought that the first C1 would be the origin of the structure. However, this is not the case. Then, how do you determine the origin for the structure? </p>",
  "messages": [
    {
      "id": "3189228",
      "postDate": "04/29/2025 01:44:15",
      "content": "<p>I am a total beginner at this. I am unclear on what determines the origin (0,0,0) of the protein structure. I would have thought that the first C1 would be the origin of the structure. However, this is not the case. Then, how do you determine the origin for the structure? </p>",
      "rawMarkdown": "I am a total beginner at this. I am unclear on what determines the origin (0,0,0) of the protein structure. I would have thought that the first C1 would be the origin of the structure. However, this is not the case. Then, how do you determine the origin for the structure?",
      "votes": null
    },
    {
      "id": "3189245",
      "postDate": "04/29/2025 02:24:51",
      "content": "<p>Hi, based on my understanding,  the origin (0,0,0) is arbitrary and not inherently linked to any specific atom like C1′.<br>\nWhen structures are predicted or experimentally solved, the absolute (x,y,z) positions are determined by how the molecule is placed during modeling or fitting — not by setting the first atom at (0,0,0).</p>",
      "rawMarkdown": "Hi, based on my understanding,  the origin (0,0,0) is arbitrary and not inherently linked to any specific atom like C1′.\nWhen structures are predicted or experimentally solved, the absolute (x,y,z) positions are determined by how the molecule is placed during modeling or fitting — not by setting the first atom at (0,0,0).",
      "votes": null
    },
    {
      "id": "3189631",
      "postDate": "04/29/2025 13:59:30",
      "content": "<p>Thanks Fae. I appreciate the input.</p>",
      "rawMarkdown": "Thanks Fae. I appreciate the input.",
      "votes": null
    },
    {
      "id": "3191624",
      "postDate": "05/01/2025 23:29:53",
      "content": "<p>Beware that Proteins and RNAs are entirely different structures. Simulation/structure prediction packages for Proteins might not work for RNAs at all. Just FYI.</p>\n<p>PS. It is a hard task for a beginner, if you do not have experience in bioinformatics. And it is not very well documented.</p>",
      "rawMarkdown": "Beware that Proteins and RNAs are entirely different structures. Simulation/structure prediction packages for Proteins might not work for RNAs at all. Just FYI.\n\nPS. It is a hard task for a beginner, if you do not have experience in bioinformatics. And it is not very well documented.",
      "votes": null
    }
  ],
  "comments": [
    {
      "id": 3189245,
      "author_name": "achievement",
      "author_url": "",
      "post_date": "04/29/2025 02:24:51",
      "content": "<p>Hi, based on my understanding,  the origin (0,0,0) is arbitrary and not inherently linked to any specific atom like C1′.<br>\nWhen structures are predicted or experimentally solved, the absolute (x,y,z) positions are determined by how the molecule is placed during modeling or fitting — not by setting the first atom at (0,0,0).</p>",
      "votes": null,
      "replies": [
        {
          "id": 3189631,
          "author_name": "pauling",
          "author_url": "",
          "post_date": "04/29/2025 13:59:30",
          "content": "<p>Thanks Fae. I appreciate the input.</p>",
          "votes": null,
          "replies": []
        }
      ]
    },
    {
      "id": 3191624,
      "author_name": "ilyakupchenko",
      "author_url": "",
      "post_date": "05/01/2025 23:29:53",
      "content": "<p>Beware that Proteins and RNAs are entirely different structures. Simulation/structure prediction packages for Proteins might not work for RNAs at all. Just FYI.</p>\n<p>PS. It is a hard task for a beginner, if you do not have experience in bioinformatics. And it is not very well documented.</p>",
      "votes": null,
      "replies": []
    }
  ],
  "raw_markdown_by_id": {
    "3189228": "I am a total beginner at this. I am unclear on what determines the origin (0,0,0) of the protein structure. I would have thought that the first C1 would be the origin of the structure. However, this is not the case. Then, how do you determine the origin for the structure?",
    "3189245": "Hi, based on my understanding,  the origin (0,0,0) is arbitrary and not inherently linked to any specific atom like C1′.\nWhen structures are predicted or experimentally solved, the absolute (x,y,z) positions are determined by how the molecule is placed during modeling or fitting — not by setting the first atom at (0,0,0).",
    "3189631": "Thanks Fae. I appreciate the input.",
    "3191624": "Beware that Proteins and RNAs are entirely different structures. Simulation/structure prediction packages for Proteins might not work for RNAs at all. Just FYI.\n\nPS. It is a hard task for a beginner, if you do not have experience in bioinformatics. And it is not very well documented."
  },
  "source": "meta"
}