trace_plot#

Script to plot one or multiple traces in 3D

Takes a trace file and either:

  • ranks traces and plots a selection

  • plots a user-selected trace in .ecsv (barcode, xyz) and PDB formats. The output files contain the trace name.

  • saves output coordinates for selected traces in PDB format so they can be loaded by other means including https://www.rcsb.org/3d-view, pymol, or nglviewer.

Future:

  • output PDBs for all the traces in a trace file

installs: pip install nglview, pdbparser

Invoke#

$ ls Trace_3D_barcode_KDtree_ROI:1.ecsv | trace_plot --pipe --selected_trace 5b1e6f89-0362-4312-a7ed-fc55ae98a0a5

this pipes the file ‘Trace_3D_barcode_KDtree_ROI:1.ecsv’ into trace_plot and then selects a trace for conversion.

$ trace_plot --input Trace_3D_barcode_KDtree_ROI:1.ecsv --all

this plots all traces in the trace file.

Format for json dict#

Please use the following format for the json dictionary to link barcode identities with different ATOM names in the PDB file:

{"12": "C  ", "18": "C  ", "9": "P  "}

keys provide barcode names in the trace file, these should be attributed to 3 character codes

pymol#

Some useful pymol commands:

set grid_mode,1
color green,  (name C*)
color red, (name P*)