Tutorial : 3D visualization with trace_plot
This script plots one or multiple traces in 3D, which can be visualized in Pymol.
How trace_plot works
trace_plot uses traces as input and either :
exports the first N traces to PDB with
–number_tracesexports one trace to PDB with
–selected_traceexports all traces to PDB with
–allsaves output coordinates for selected traces in PDB format
Input
Name of the trace file: merged_traces.ecsv
[27]:
import matplotlib.pyplot as plt
import matplotlib.image as mpimg
%matplotlib inline
data_path = "/mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2"
dest_path = f"{data_path}/output"
input_trace = f"{dest_path}/merged_traces.ecsv"
print(f"Input: {input_trace}")
Input: /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/merged_traces.ecsv
Step 1 : export traces in PDB format
Example 1: Export the first N traces
By default, trace_plot exports a limited number of traces from the input trace file to PDB files. With the option --number_traces or -n we can choose the number of traces to export. Here we will take the first 100 traces.
A json file in the following format : {“12”: “C “, “18”: “N “, “9”: “P “} used with --barcode_type_dict will later allow us to color code the barcodes in pymol.
[51]:
output_pdb = f"{dest_path}/first_100_PDBs"
json_file = f"{dest_path}/bcd.json"
!trace_plot --input {input_trace} --number_traces 100 --barcode_type_dict {json_file} --output {output_pdb}
------- Running trace_plot.py --------
Plot one or multiple traces in 3D.
File does not exist
! [INFO] Folder '/mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs' already exists.
1 trace files to process= /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/merged_traces.ecsv
$ Importing table from pyHiM format
Successfully loaded trace table: /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/merged_traces.ecsv
$ number of traces available: 1792
$ number of traces to process: 100
Converting trace ID: 0001dad5-dce3-44c1-b178-b1be008c7b99
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0001dad5-dce3-44c1-b178-b1be008c7b99.pdb with 45 atoms.
Converting trace ID: 001b4acb-c02e-4678-b4dd-a00879041456
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/001b4acb-c02e-4678-b4dd-a00879041456.pdb with 47 atoms.
Converting trace ID: 00518048-a9cd-4ada-96da-31bba0bf0722
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/00518048-a9cd-4ada-96da-31bba0bf0722.pdb with 52 atoms.
Converting trace ID: 00693531-76fe-41d2-a59c-0e1d5351aeb0
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/00693531-76fe-41d2-a59c-0e1d5351aeb0.pdb with 51 atoms.
Converting trace ID: 00912b39-61dc-42ef-9ca3-f34137293dca
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/00912b39-61dc-42ef-9ca3-f34137293dca.pdb with 65 atoms.
Converting trace ID: 009cb334-0c13-4eee-93e1-b7272fdc3b9d
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/009cb334-0c13-4eee-93e1-b7272fdc3b9d.pdb with 53 atoms.
Converting trace ID: 00bce5b6-02e3-40c3-9bcf-5dae783c5f06
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/00bce5b6-02e3-40c3-9bcf-5dae783c5f06.pdb with 56 atoms.
Converting trace ID: 0143d6fd-5373-4734-9686-59062527d2c9
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0143d6fd-5373-4734-9686-59062527d2c9.pdb with 61 atoms.
Converting trace ID: 016d4d62-51b8-46ed-999f-4fd26255c17b
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/016d4d62-51b8-46ed-999f-4fd26255c17b.pdb with 61 atoms.
Converting trace ID: 01988932-d667-448f-a29d-45e55c67f50d
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/01988932-d667-448f-a29d-45e55c67f50d.pdb with 51 atoms.
Converting trace ID: 01acc95b-f9ff-477f-b639-947d36b7b2bf
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/01acc95b-f9ff-477f-b639-947d36b7b2bf.pdb with 57 atoms.
Converting trace ID: 01e31f5f-d696-487d-b891-a94af776bffa
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/01e31f5f-d696-487d-b891-a94af776bffa.pdb with 44 atoms.
Converting trace ID: 021469e6-0912-4eec-ae64-8b6a64b83daa
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/021469e6-0912-4eec-ae64-8b6a64b83daa.pdb with 68 atoms.
Converting trace ID: 023169dd-8cbf-471e-a935-d104ee2cc8e8
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/023169dd-8cbf-471e-a935-d104ee2cc8e8.pdb with 54 atoms.
Converting trace ID: 02469f4a-afe8-4487-ac06-cc523b57ff31
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/02469f4a-afe8-4487-ac06-cc523b57ff31.pdb with 65 atoms.
Converting trace ID: 026e6240-ac86-46d9-a5c0-4c1116c50efd
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/026e6240-ac86-46d9-a5c0-4c1116c50efd.pdb with 68 atoms.
Converting trace ID: 027d40fa-281b-436b-834e-570187d74c89
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/027d40fa-281b-436b-834e-570187d74c89.pdb with 29 atoms.
Converting trace ID: 02c34737-2edf-489c-9c7b-b76c75b8e1ca
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/02c34737-2edf-489c-9c7b-b76c75b8e1ca.pdb with 49 atoms.
Converting trace ID: 02d1aebe-58c8-4c4f-af1e-2ec31b28a738
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/02d1aebe-58c8-4c4f-af1e-2ec31b28a738.pdb with 58 atoms.
Converting trace ID: 02def7ff-b0b6-4175-9454-d4b2b1bc089c
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/02def7ff-b0b6-4175-9454-d4b2b1bc089c.pdb with 54 atoms.
Converting trace ID: 02fe46e2-9af1-4448-9e56-6458bdc875ac
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/02fe46e2-9af1-4448-9e56-6458bdc875ac.pdb with 65 atoms.
Converting trace ID: 0328f281-514a-47a9-bdd0-9df4ffce20d7
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0328f281-514a-47a9-bdd0-9df4ffce20d7.pdb with 50 atoms.
Converting trace ID: 033cac1c-fc53-4806-bb61-1cc26b1d33ea
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/033cac1c-fc53-4806-bb61-1cc26b1d33ea.pdb with 51 atoms.
Converting trace ID: 034923e9-d66a-46fe-b0fd-b60195f73da1
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/034923e9-d66a-46fe-b0fd-b60195f73da1.pdb with 53 atoms.
Converting trace ID: 034e8b8a-bcb7-4916-937d-16047af2794b
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/034e8b8a-bcb7-4916-937d-16047af2794b.pdb with 45 atoms.
Converting trace ID: 039b8a0a-2d1a-44bd-bb36-678b7af95c5e
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/039b8a0a-2d1a-44bd-bb36-678b7af95c5e.pdb with 58 atoms.
Converting trace ID: 03b171ee-0b94-45b5-93ff-102f485ec0eb
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/03b171ee-0b94-45b5-93ff-102f485ec0eb.pdb with 46 atoms.
Converting trace ID: 03b21244-6b39-4277-89f6-0ce0de4de5e9
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/03b21244-6b39-4277-89f6-0ce0de4de5e9.pdb with 51 atoms.
Converting trace ID: 03b28a69-8ad9-42dc-a038-748c6292a0da
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/03b28a69-8ad9-42dc-a038-748c6292a0da.pdb with 62 atoms.
Converting trace ID: 03f6bef2-2d69-447d-a7e7-e73857b361c5
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/03f6bef2-2d69-447d-a7e7-e73857b361c5.pdb with 58 atoms.
Converting trace ID: 03fe332d-45d8-4f8c-b268-033e22343107
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/03fe332d-45d8-4f8c-b268-033e22343107.pdb with 67 atoms.
Converting trace ID: 040d9c4c-729f-461d-9f70-22ab77980cfe
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/040d9c4c-729f-461d-9f70-22ab77980cfe.pdb with 59 atoms.
Converting trace ID: 041c26ab-9d2b-4cf2-8a98-39245cb179d7
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/041c26ab-9d2b-4cf2-8a98-39245cb179d7.pdb with 63 atoms.
Converting trace ID: 04433131-67b2-46b1-a740-4e16e8561896
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/04433131-67b2-46b1-a740-4e16e8561896.pdb with 64 atoms.
Converting trace ID: 046a0731-1c77-4cd4-9176-e6ad89760219
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/046a0731-1c77-4cd4-9176-e6ad89760219.pdb with 49 atoms.
Converting trace ID: 04736e82-9aa6-4ded-96a2-323966b0a5c9
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/04736e82-9aa6-4ded-96a2-323966b0a5c9.pdb with 50 atoms.
Converting trace ID: 04b3c103-d6a6-411b-a347-1211ec92187a
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/04b3c103-d6a6-411b-a347-1211ec92187a.pdb with 43 atoms.
Converting trace ID: 04d9cc13-839c-4638-9752-a68200387c37
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/04d9cc13-839c-4638-9752-a68200387c37.pdb with 51 atoms.
Converting trace ID: 04f530ed-a61b-4c9e-9c6b-39daff1eb6d8
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/04f530ed-a61b-4c9e-9c6b-39daff1eb6d8.pdb with 54 atoms.
Converting trace ID: 0541b340-6f1e-40d2-9d74-ee245edcdbdb
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0541b340-6f1e-40d2-9d74-ee245edcdbdb.pdb with 67 atoms.
Converting trace ID: 054ab387-a4a6-4a3b-921d-05ca12fdec04
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/054ab387-a4a6-4a3b-921d-05ca12fdec04.pdb with 51 atoms.
Converting trace ID: 05b0a52f-facc-43ac-9255-6a710bc04892
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/05b0a52f-facc-43ac-9255-6a710bc04892.pdb with 47 atoms.
Converting trace ID: 05b91c3c-72ea-483b-9dbf-edeeb1f856b4
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/05b91c3c-72ea-483b-9dbf-edeeb1f856b4.pdb with 55 atoms.
Converting trace ID: 05f88815-34fa-4f04-8bd2-14884eafd47e
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/05f88815-34fa-4f04-8bd2-14884eafd47e.pdb with 69 atoms.
Converting trace ID: 06430cbb-745d-41cf-8b84-a435aba2e1f4
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/06430cbb-745d-41cf-8b84-a435aba2e1f4.pdb with 51 atoms.
Converting trace ID: 066144ee-9ea7-4ac2-9dd3-26069baaa756
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/066144ee-9ea7-4ac2-9dd3-26069baaa756.pdb with 38 atoms.
Converting trace ID: 067d0b3a-1843-41fb-bcd9-0d7e59f4bca6
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/067d0b3a-1843-41fb-bcd9-0d7e59f4bca6.pdb with 63 atoms.
Converting trace ID: 06807b19-658d-4630-b62c-ea3d4a09b3e3
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/06807b19-658d-4630-b62c-ea3d4a09b3e3.pdb with 63 atoms.
Converting trace ID: 0694aa4d-5e3f-43eb-bbae-30af2c01423f
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0694aa4d-5e3f-43eb-bbae-30af2c01423f.pdb with 63 atoms.
Converting trace ID: 06b45239-762b-4171-a749-98a0050fdacc
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/06b45239-762b-4171-a749-98a0050fdacc.pdb with 45 atoms.
Converting trace ID: 06d6ca7b-56e9-455e-ab19-4ce53e27c2cb
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/06d6ca7b-56e9-455e-ab19-4ce53e27c2cb.pdb with 65 atoms.
Converting trace ID: 06fa36ce-3c40-48a5-9c0a-be07317680ce
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/06fa36ce-3c40-48a5-9c0a-be07317680ce.pdb with 52 atoms.
Converting trace ID: 0723155d-a285-4421-b0ca-fd56c9a0a5d8
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0723155d-a285-4421-b0ca-fd56c9a0a5d8.pdb with 50 atoms.
Converting trace ID: 074f3fcd-b872-43a9-8198-f50658005b39
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/074f3fcd-b872-43a9-8198-f50658005b39.pdb with 59 atoms.
Converting trace ID: 0768461e-6be5-43dd-86f2-d30b665ccf39
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0768461e-6be5-43dd-86f2-d30b665ccf39.pdb with 65 atoms.
Converting trace ID: 07c3064b-2ce3-4db0-8bb1-62714b9ccc38
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/07c3064b-2ce3-4db0-8bb1-62714b9ccc38.pdb with 54 atoms.
Converting trace ID: 07c63c1a-7d3c-49c4-a01d-639e8c61c325
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/07c63c1a-7d3c-49c4-a01d-639e8c61c325.pdb with 50 atoms.
Converting trace ID: 07d4a1e6-1ac3-4eed-9993-81de4e21cc11
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/07d4a1e6-1ac3-4eed-9993-81de4e21cc11.pdb with 62 atoms.
Converting trace ID: 07d4d792-a1fb-4289-bacd-7012efa8f3fa
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/07d4d792-a1fb-4289-bacd-7012efa8f3fa.pdb with 60 atoms.
Converting trace ID: 07de3902-6e56-4fd9-b62c-05eef193d9df
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/07de3902-6e56-4fd9-b62c-05eef193d9df.pdb with 51 atoms.
Converting trace ID: 07f417d9-339d-43ae-8350-05fb7d93e7cb
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/07f417d9-339d-43ae-8350-05fb7d93e7cb.pdb with 59 atoms.
Converting trace ID: 08135774-6775-4f3f-99a1-fbead2f1e034
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/08135774-6775-4f3f-99a1-fbead2f1e034.pdb with 38 atoms.
Converting trace ID: 0828adc7-a13f-4846-b8cc-961f1031e387
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0828adc7-a13f-4846-b8cc-961f1031e387.pdb with 54 atoms.
Converting trace ID: 0831ada0-8816-48d0-88d7-b3d3e29b71f2
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0831ada0-8816-48d0-88d7-b3d3e29b71f2.pdb with 62 atoms.
Converting trace ID: 083e2034-405e-454f-a4d5-66f717af2392
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/083e2034-405e-454f-a4d5-66f717af2392.pdb with 53 atoms.
Converting trace ID: 086ea8b0-5e2a-4401-9c37-181519111956
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/086ea8b0-5e2a-4401-9c37-181519111956.pdb with 62 atoms.
Converting trace ID: 08d8d8f6-9c01-4fe6-a4f2-6ffaf3503543
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/08d8d8f6-9c01-4fe6-a4f2-6ffaf3503543.pdb with 54 atoms.
Converting trace ID: 0919b0fd-8ee2-466f-8827-6a1937646e61
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0919b0fd-8ee2-466f-8827-6a1937646e61.pdb with 69 atoms.
Converting trace ID: 092248d6-3e8c-4a3c-be9b-c28d7a959c8e
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/092248d6-3e8c-4a3c-be9b-c28d7a959c8e.pdb with 52 atoms.
Converting trace ID: 09585735-bccf-423a-969d-33960cb0e347
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/09585735-bccf-423a-969d-33960cb0e347.pdb with 40 atoms.
Converting trace ID: 095e4990-18c5-4c88-bd38-fc616f181f5a
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/095e4990-18c5-4c88-bd38-fc616f181f5a.pdb with 64 atoms.
Converting trace ID: 0988d438-9fd6-4def-81b5-ed5477de96ea
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0988d438-9fd6-4def-81b5-ed5477de96ea.pdb with 38 atoms.
Converting trace ID: 09beb8a2-f057-41ad-aa47-b363131573e3
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/09beb8a2-f057-41ad-aa47-b363131573e3.pdb with 58 atoms.
Converting trace ID: 0a14a086-f3dd-4e7b-8eee-0ab688382f42
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0a14a086-f3dd-4e7b-8eee-0ab688382f42.pdb with 42 atoms.
Converting trace ID: 0a1923b8-3451-43ae-8e1a-f6cadb2ba64a
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0a1923b8-3451-43ae-8e1a-f6cadb2ba64a.pdb with 50 atoms.
Converting trace ID: 0a66f706-f673-4c13-ba77-01a7ce4917c1
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0a66f706-f673-4c13-ba77-01a7ce4917c1.pdb with 54 atoms.
Converting trace ID: 0a92f17f-b246-477a-ab66-5b44ab0907ea
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0a92f17f-b246-477a-ab66-5b44ab0907ea.pdb with 41 atoms.
Converting trace ID: 0aabf719-0031-4896-b40e-880a81d49c5b
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0aabf719-0031-4896-b40e-880a81d49c5b.pdb with 59 atoms.
Converting trace ID: 0ab4af07-f80b-4196-98a5-8dc23aa4bf4e
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0ab4af07-f80b-4196-98a5-8dc23aa4bf4e.pdb with 56 atoms.
Converting trace ID: 0ac9d520-e88e-4f7e-ba4b-32879c5896d1
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0ac9d520-e88e-4f7e-ba4b-32879c5896d1.pdb with 61 atoms.
Converting trace ID: 0ad2849a-a826-40bb-8004-40df26bec8d2
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0ad2849a-a826-40bb-8004-40df26bec8d2.pdb with 41 atoms.
Converting trace ID: 0ad7bdd6-872c-45f6-8292-2e7bc85f101f
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0ad7bdd6-872c-45f6-8292-2e7bc85f101f.pdb with 65 atoms.
Converting trace ID: 0b4a0e39-ad0d-47f5-bd4d-8a7bc1161327
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0b4a0e39-ad0d-47f5-bd4d-8a7bc1161327.pdb with 54 atoms.
Converting trace ID: 0b52f734-d315-4e8f-83db-07fe091bc2be
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0b52f734-d315-4e8f-83db-07fe091bc2be.pdb with 47 atoms.
Converting trace ID: 0b6d6c08-dfae-47ca-a202-2e10f7a34549
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0b6d6c08-dfae-47ca-a202-2e10f7a34549.pdb with 53 atoms.
Converting trace ID: 0bcd5a7f-83b4-45f4-978c-f6d22e64bc91
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0bcd5a7f-83b4-45f4-978c-f6d22e64bc91.pdb with 39 atoms.
Converting trace ID: 0c054933-ff99-4b83-970a-ade40859b4ef
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0c054933-ff99-4b83-970a-ade40859b4ef.pdb with 56 atoms.
Converting trace ID: 0c27677e-ddfa-4a99-ad1e-ecedf8bbe674
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0c27677e-ddfa-4a99-ad1e-ecedf8bbe674.pdb with 53 atoms.
Converting trace ID: 0c3e9a08-b340-4e6a-8b8b-649707cf5943
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0c3e9a08-b340-4e6a-8b8b-649707cf5943.pdb with 56 atoms.
Converting trace ID: 0c5de811-cc7b-4931-a572-430528f9ddcd
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0c5de811-cc7b-4931-a572-430528f9ddcd.pdb with 54 atoms.
Converting trace ID: 0c7bdc14-b975-4051-8962-e6799a4067eb
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0c7bdc14-b975-4051-8962-e6799a4067eb.pdb with 65 atoms.
Converting trace ID: 0ca36bac-fd96-44bb-8d45-5b08e5bd0ddf
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0ca36bac-fd96-44bb-8d45-5b08e5bd0ddf.pdb with 62 atoms.
Converting trace ID: 0ca685a4-655d-4269-9fa8-e17b2ffa452d
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0ca685a4-655d-4269-9fa8-e17b2ffa452d.pdb with 55 atoms.
Converting trace ID: 0cb3a0cb-cab5-43b8-b0a8-609a50d01a73
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0cb3a0cb-cab5-43b8-b0a8-609a50d01a73.pdb with 57 atoms.
Converting trace ID: 0cf61e71-8780-4128-93e5-df22467f1071
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0cf61e71-8780-4128-93e5-df22467f1071.pdb with 34 atoms.
Converting trace ID: 0cfbc978-d53f-46e5-a2bc-1a560e781367
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0cfbc978-d53f-46e5-a2bc-1a560e781367.pdb with 67 atoms.
Converting trace ID: 0d032130-11a8-484c-9af2-1a98740fd965
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0d032130-11a8-484c-9af2-1a98740fd965.pdb with 64 atoms.
Converting trace ID: 0d145d64-ba09-4d9c-97bc-227c28c9b836
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0d145d64-ba09-4d9c-97bc-227c28c9b836.pdb with 24 atoms.
Converting trace ID: 0d5561fe-2c7f-4537-867c-60ed1c2f8fd9
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0d5561fe-2c7f-4537-867c-60ed1c2f8fd9.pdb with 30 atoms.
Converting trace ID: 0dfd529b-0cc0-45fb-b4f9-0b5834666e87
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/first_100_PDBs/0dfd529b-0cc0-45fb-b4f9-0b5834666e87.pdb with 53 atoms.
Processed <1> trace file(s)
Finished execution
The output files are named after each exported Trace_ID. The first 100 traces are saved to the folder {dest_paht}/first_100_PDBs/.
Example 2 : Export one trace
Use selected_trace to select a trace from your trace table. The option--number_traces is then ignored when ‘selected_trace` is used.
[49]:
json_file = f"{dest_path}/bcd.json"
! ls {input_trace} | trace_plot --pipe --selected_trace 0dfd529b-0cc0-45fb-b4f9-0b5834666e87 --output {dest_path} --barcode_type_dict {json_file}
------- Running trace_plot.py --------
Plot one or multiple traces in 3D.
File does not exist
! [INFO] Folder '/mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output' already exists.
1 trace files to process= /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/merged_traces.ecsv
$ Importing table from pyHiM format
Successfully loaded trace table: /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/merged_traces.ecsv
$ number of traces available: 1792
$ number of traces to process: 1
Converting trace ID: 0dfd529b-0cc0-45fb-b4f9-0b5834666e87
No barcode_type dictionary provided. Assigning one unique atom name per barcode.
Done writing /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/0dfd529b-0cc0-45fb-b4f9-0b5834666e87.pdb with 53 atoms.
Processed <1> trace file(s)
Finished execution
Step 2 : 3D Visualization in pymol
Previously with trace_plot we generated a folder with PDB files containing the 3D coordinates of the traces. Each barcode is assigned a different ATOM name, which is then used in pymol to color code barcodes. The generated PDB files will be loaded in pymol.
For this you need to first install pymol.
Then in the top box you will find a terminal where you can write text, starting with PyMOL> . In this terminal you will write the following commands:
Terminal commands in pymol
The first line will load the functions from a python script in traceratops. Change “/home/user/Repositories/” with the location of your traceratops repository :
$ run /home/user/Repositories/traceratops/traceratops/pymol_script.py
The second command will load 100 structures from the PDB file and represent them in a grid.
$ load_pdb_grid /mnt/grey/DATA/users/zidoum/traceraptops/data/Boettiger/Replicate2/output/
The third line will color code each barcode with a different color.
$ color_all_barcodes()
The final line will make the structures spin.
$ spin_grid
[52]:
# Example of what you should be visualizing in pymol
screenchot2 = f"{dest_path}/pymol_structures.png"
screenshot3 = f"{dest_path}/pymol_100_strcutures.png"
fig, axes = plt.subplots(1, 2, figsize=(25, 10))
for ax, path,title in zip(axes, [screenshot2, screenshot3],["Single trace in 3D", "100 traces in 3D"]):
ax.set_title(title, fontsize=20)
img = mpimg.imread(path)
ax.imshow(img)
ax.axis("off")
plt.tight_layout()
plt.show()
Color code barcodes (atoms)
If the user provided a json dictionary (as seen above), these are used as ATOM names. The json file has to be in the following format to link barcode identities with different ATOM names in the PDB file:
{“12”: “C “, “18”: “N “, “9”: “P “}
Keys provide barcode names in the trace file, these should be attributed to 3 character codes. In this example, the barcode 12 is assigned the ATOM name C, barcode 18 is assigned N and atom 9 is assigned P. This provides a useful way of colorcoding your barcodes using a user defined coloring code.
In this case you can run the first two lines of the script above (plot_traces and pymol terminal lines) and then apply separate colors for each barcode as follows as follows in the pymol terminal:
$ set grid_mode,1
$ color green, (name C*)
$ color red, (name P*)
$ color yellow, (name N*)
Summary
Visualize traces in pymol with trace_plot
Option |
Use |
|---|---|
-n |
Number of traces used |
-N |
Minimum number of barcodes for traces selected |
–selected_traces |
Select traces for analysis |
–all |
Select all traces |
–barcode_type_dict |
Json dictionary linking barcodes and atom types (MUST BE 3 characters long!) |
-O |
Output tag |