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Dimple anode viewer does not focus on blobs

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評估

難度
3/5
預估耗時
1-2 天
新手友好度
65/100
Issue 類型
缺陷
描述清晰度
基本清楚
活躍度
活躍
技術堆疊
python
領域
data-visualization

研究方向

Look for the dimple anode viewer code, likely in a file related to dimple or viewer. The provided helper function shows how to focus on an isosurface. Find where the viewer currently focuses on the nearest atom and modify it to use the isosurface focus method. Test by running the viewer with anomalous density blobs to ensure the view centers on the blob.

由索引模型根據 Issue 內容生成。

描述

The dimpe anode viewer focusses on the nearest atom to the blob. In cases of unmodelled anomalous density, the blob can be outside of the focussed view as it picks the nearest atom.

Encountered a similar problem when making the metal_iid viewer and solved it with this helper function, which focusses on the isosurface itself rather than the nearest atom:

def generate_isosurfaces_and_focus_on_current_peak(
    builder: mvs.Builder,
    peaks: list[Peak],
    focus_peak_num: int,
    isovalue=5,
):
    for peak_num, _ in enumerate(peaks, start=1):
        # Add anomalous double difference map for the current peak
        ccp4 = builder.download(url=f"map{peak_num}").parse(format="map")
        isosurface_peak = (
            ccp4.volume()
            .representation(
                type="isosurface",
                relative_isovalue=isovalue,
                show_wireframe=True,
                show_faces=False,
            )
            .color(color="#da21fa")
            .opacity(opacity=0.25)
        )
        if peak_num == focus_peak_num:
            isosurface_peak.focus()  # focus on the current peak site

        # Add 2FO-FC map for the current peak
        ccp4_2fo_fc = builder.download(url=f"fmap{peak_num}").parse(format="map")
        ccp4_2fo_fc.volume().representation(
            type="isosurface",
            relative_isovalue=1.5,
            show_wireframe=True,
            show_faces=False,
        ).color(color="#2f78d7").opacity(opacity=0.25)
def generate_isosurfaces_and_focus_on_current_peak(
    builder: mvs.Builder,
    peaks: list[Peak],
    focus_peak_num: int,
    isovalue=5,
):
    for peak_num, _ in enumerate(peaks, start=1):
        # Add anomalous double difference map for the current peak
        ccp4 = builder.download(url=f"map{peak_num}").parse(format="map")
        isosurface_peak = (
            ccp4.volume()
            .representation(
                type="isosurface",
                relative_isovalue=isovalue,
                show_wireframe=True,
                show_faces=False,
            )
            .color(color="#da21fa")
            .opacity(opacity=0.25)
        )
        if peak_num == focus_peak_num:
            isosurface_peak.focus()  # focus on the current peak site

        # Add 2FO-FC map for the current peak
        ccp4_2fo_fc = builder.download(url=f"fmap{peak_num}").parse(format="map")
        ccp4_2fo_fc.volume().representation(
            type="isosurface",
            relative_isovalue=1.5,
            show_wireframe=True,
            show_faces=False,
        ).color(color="#2f78d7").opacity(opacity=0.25)
主要語言
Python
星號
2
分支
3
平均合併
1 天 6 小時
30 天內合併 PR
4

環境準備

  • 提供 Dockerfile 或 Docker Compose 檔案
  • 沒有 Pull Request 範本
  • 沒有貢獻指南

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  3. Fork 儲存庫，在一個分支上完成修改。
  4. 送出 Pull Request，並在描述裡引用這個 Issue 編號。

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