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Dimple anode viewer does not focus on blobs

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难度
3/5
预计耗时
1-2 天
新手友好度
65/100
Issue 类型
缺陷
描述清晰度
基本清楚
活跃度
活跃
技术栈
python
领域
data-visualization

调研方向

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.

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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)
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  3. Fork 仓库，在一个分支上完成修改。
  4. 提交 Pull Request，并在描述里引用这个 Issue 编号。

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