# 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

```bash
$ 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.

```bash
$ 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*)
```