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feat: render mutated residues as spheres in ChimeraX plots for better… #107

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Merged
St3451 merged 2 commits into from
May 28, 2026
Merged

feat: render mutated residues as spheres in ChimeraX plots for better… #107

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ff9917b
feat: render mutated residues as spheres in ChimeraX plots for better…
St3451 May 28, 2026
129e3ae
feat: optimize handling of mutated positions for ChimeraX plots by re…
St3451 May 28, 2026
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50 changes: 37 additions & 13 deletions scripts/plotting/chimerax_plot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -139,22 +139,23 @@ def get_palette(intervals, type="diverging"):
return f"{intervals[0]},#FFFFB2:{intervals[1]},#FECC5C:{intervals[2]},#FD8D3C:{intervals[3]},#F03B20:{intervals[4]},#BD0026"


def get_chimerax_command(chimerax_bin,
pdb_path,
chimera_output_path,
attr_file_path,
attribute,
intervals,
gene,
def get_chimerax_command(chimerax_bin,
pdb_path,
chimera_output_path,
attr_file_path,
attribute,
intervals,
gene,
uni_id,
labels,
i,
f,
cohort="",
clusters=None,
colored_positions=None,
pixelsize=0.1,
transparent_bg=False):

palette = get_palette(intervals, type="diverging") if attribute == "logscore" else get_palette(intervals, type="sequential")
transparent_bg_suffix = " transparentBackground true" if transparent_bg else ""

Expand Down Expand Up @@ -185,6 +186,20 @@ def get_chimerax_command(chimerax_bin,
"zoom;"
)

# Render mutated (= colored) residues as spheres so their colour is actually
# visible on the cartoon. Without this, the colour mapping is washed out by
# the cartoon ribbon. ~sel afterwards clears the green selection markers
# from the saved image.
if colored_positions is not None and len(colored_positions) > 0:
pos_selector = ",".join(str(int(p)) for p in sorted(set(colored_positions)))
chimerax_script += (
f"sel :{pos_selector};"
"style sel sphere;"
"hide sel cartoons;"
"show sel atoms;"
"~sel;"
)

if clusters is not None and len(clusters) > 0:
for pos in clusters:
chimerax_script += f"marker #10 position :{pos} color #dacae961 radius 5.919;"
Expand Down Expand Up @@ -276,19 +291,26 @@ def generate_chimerax_plot(output_dir,
continue

if pdb_path:


# Mutated rows = rows the .defattr file is written from = the
# residues that actually receive a colour from `color byattribute`.
# Compute once and reuse so the sphere-render selection stays
# coupled to the .defattr contents.
result_gene_mutated = result_gene.dropna()
colored_positions = result_gene_mutated["Pos"].astype(int).tolist()

for attribute in ["mutres", "mutvol", "score", "logscore"]:

logger.debug("Generating attribute files..")
attr_file_path = f"{chimera_attr_path}/{gene}_{attribute}.defattr"
create_attribute_file(path_to_file=attr_file_path,
df=result_gene.dropna(),
df=result_gene_mutated,
attribute_col=cols[attribute],
attribute_name=attribute)

attribute_vector = result_gene[cols[attribute]]
intervals = get_intervals(attribute_vector, attribute)

logger.debug("Generating 3D images..")
try:
chimerax_command = get_chimerax_command(chimerax_bin,
Expand All @@ -303,6 +325,7 @@ def generate_chimerax_plot(output_dir,
i,
f,
cohort,
colored_positions=colored_positions,
pixelsize=pixel_size,
transparent_bg=transparent_bg)
except ValueError as exc:
Expand All @@ -326,6 +349,7 @@ def generate_chimerax_plot(output_dir,
f,
cohort,
clusters=clusters,
colored_positions=colored_positions,
pixelsize=pixel_size,
transparent_bg=transparent_bg)
except ValueError as exc:
Expand Down