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Dimple anode viewer does not focus on blobs

Abierto
  • ¿Algo no está bien?
#392 0 comentarios 0 reacciones 0 asignados Ver en GitHub

Nadie ha tomado este issue todavía.

Evaluación

Dificultad
3/5
Tiempo estimado
1-2 días
Aptitud para principiantes
65/100
Tipo de issue
Error
Claridad
Bastante claro
Estado de actividad
Activo
Stack tecnológico
python
Área
data-visualization

Línea de trabajo

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.

Escrito por el modelo de indexación a partir del texto del issue.

Descripción

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)
Lenguaje dominante
Python
Estrellas
2
Forks
3
Merge medio
1 d 14 h
PR fusionados (30 d)
5

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  • Incluye un Dockerfile o un archivo de Docker Compose
  • Sin plantilla de pull request
  • Sin guía de contribución

Primeros pasos

  1. Lee el issue completo y luego la guía de contribución del proyecto.
  2. Comenta en el issue que vas a ocuparte — evita que dos personas hagan lo mismo.
  3. Haz un fork del repositorio y trabaja en una rama.
  4. Abre un pull request que haga referencia al número del issue.

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