VisualPhysiologyDB · k-wavy · Mar 10, 2026 · Jan 29, 2026 · Feb 3, 2026 · Feb 18, 2026
diff --git a/README.md b/README.md
diff --git a/data/cached_structures/1U19.pdb b/data/cached_structures/1U19.pdb
diff --git a/data/website/index.html b/data/website/index.html
diff --git a/examples/custom_annotation_ex/1U19.pdb b/examples/custom_annotation_ex/1U19.pdb
diff --git a/examples/custom_annotation_ex/optics_custom_annotations_ex.csv b/examples/custom_annotation_ex/optics_custom_annotations_ex.csv
@@ -0,0 +1,6 @@
+position,color,style,label
+124,red,sphere,M124T (Missense)
+296,yellow,stick,Retinal Site
+10,blue,cartoon,N-Terminus
+11,blue,cartoon,
+12,blue,cartoon,
diff --git a/examples/custom_annotation_ex/visualize_optics_custom_annotations_ex.pml b/examples/custom_annotation_ex/visualize_optics_custom_annotations_ex.pml
@@ -0,0 +1,33 @@
+# OPTICS Structure Annotation Script
+load 1U19.pdb
+hide everything
+bg_color white
+show cartoon, chain A
+color white, chain A
+set cartoon_transparency, 0.2, chain A
+
+# --- Annotations ---
+select site_124, chain A and resi 124
+color red, site_124
+show spheres, site_124
+set sphere_scale, 1.2, site_124
+label site_124 and n. ca, 'M124T (Missense)'
+select site_296, chain A and resi 296
+color yellow, site_296
+show sticks, site_296
+label site_296 and n. ca, 'Retinal Site'
+select site_10, chain A and resi 10
+color blue, site_10
+set cartoon_transparency, 0.0, site_10
+label site_10 and n. ca, 'N-Terminus'
+select site_11, chain A and resi 11
+color blue, site_11
+set cartoon_transparency, 0.0, site_11
+select site_12, chain A and resi 12
+color blue, site_12
+set cartoon_transparency, 0.0, site_12
+
+# --- Final Settings ---
+deselect
+orient
+ray 1000, 1000
diff --git a/examples/custom_annotation_ex/visualize_optics_custom_annotations_ex_chimerax.cxc b/examples/custom_annotation_ex/visualize_optics_custom_annotations_ex_chimerax.cxc
@@ -0,0 +1,27 @@
+# OPTICS Structure Annotation Script (ChimeraX)
+open 1U19.pdb
+hide atoms
+hide cartoons
+set bgColor black
+show /A cartoons
+color /A gray
+transparency /A 20 target c
+
+# --- Annotations ---
+color /A:124 red
+show /A:124 atoms
+style /A:124 sphere
+label /A:124 text "M124T (Missense)"
+color /A:296 yellow
+show /A:296 atoms
+style /A:296 stick
+label /A:296 text "Retinal Site"
+color /A:10 blue
+transparency /A:10 0 target c
+label /A:10 text "N-Terminus"
+color /A:11 blue
+transparency /A:11 0 target c
+color /A:12 blue
+transparency /A:12 0 target c
+
+view
diff --git a/examples/ex_structures/C_phantasticus_LWS1_esmfold.pdb b/examples/ex_structures/C_phantasticus_LWS1_esmfold.pdb
diff --git a/examples/ex_structures/C_phantasticus_LWS2_esmfold.pdb b/examples/ex_structures/C_phantasticus_LWS2_esmfold.pdb
diff --git a/examples/ex_structures/structural_validation_results.csv b/examples/ex_structures/structural_validation_results.csv
@@ -0,0 +1,3 @@
+accession,sequence_length,mapped_lysine_pdb_id,backbone_rmsd,lysine_nz_distance_A
+C_phantasticus_LWS1,359,310,9.250225342988399,3.3669949
+C_phantasticus_LWS2,354,307,8.915429050281164,4.109282
diff --git a/examples/optics_on_fish_paralog_test_2026-03-10_13-13-45/arg_log.txt b/examples/optics_on_fish_paralog_test_2026-03-10_13-13-45/arg_log.txt
@@ -0,0 +1,17 @@
+Selected Options...
+input_sequence: D:/safra/Github/optics/examples/optics_struct_comparison_ex.fasta
+report_dir: D:\safra\Github\optics\examples/optics_on_fish_paralog_test_2026-03-10_13-13-45
+output_file: fish_paralog_test
+model: whole-dataset-mnm
+encoding_method: aa_prop
+tolerate_non_standard_aa: True
+tolerate_incomplete_seqs: False
+blastp: True
+	blastp_report: blastp_report.txt
+	refseq: bovine
+	custom_ref_file: None
+bootstrap: True
+	visualize_bootstrap: True
+		bootstrap_viz_file: bootstrap_viz
+		save_as: svg
+		full_spectrum_xaxis: False
diff --git a/examples/optics_on_fish_paralog_test_2026-03-10_13-13-45/blastp_report.csv b/examples/optics_on_fish_paralog_test_2026-03-10_13-13-45/blastp_report.csv
@@ -0,0 +1,3 @@
+query_id,status,closest_match_id,match_species,match_opsin_family,match_accession,match_lambda_max,percent_identity,alignment_length,mismatches,gap_opens,e_value,differences_from_match
+C_phantasticus_LWS2,Success,S698,lwsanc_pigmenti_sp.,LWS,lwsanc_pigmenti,564.0,79.251,347,71,1,0.0,E2D; A6E; I8A; N14S; V25E; D30H; A39L; C40T; T41S; L52V; V81I; I84L; I88V; I95V; I111V; Y115F; V116T; V119T; A123T; G124A; V130I; R147K; W152L; T154A; I158V; I162V; A164S; I165A; L166V; K201Q; T206V; L208M; F209I; L214I; V218I; I221L; F225Q; S228W; H231R; S232A; R248K; T251S; I255V; V258I; F261Y; V262C; I263F; A269T; T270F; T273C; S275A; C277A; W283F; T287A; S289A; L290M; G297S; L318M; E329D; I334V; T335S; S337T; T339K; T344S; A345V; -347P; -348A
+C_phantasticus_LWS1,Success,S197,Carassius_auratus,LWS,L11867.1,560.9,85.794,359,49,2,0.0,I8M; D25E; I39L; V46F; I49V; L50A; I84L; I89L; V96T; I99F; Y100F; L109M; I112F; Y115F; A118S; A119V; I137V; E150A; T154S; T160S; L165A; F166I; Y178F; N195S; R201Q; V205I; T206V; L209I; L214I; S217A; V218I; F221L; C225A; M228L; A232T; L259F; F271C; V272A; G275A; T276A; Y278N; Y318M; M320L
diff --git a/examples/optics_on_fish_paralog_test_2026-03-10_13-13-45/bootstrap_viz_part1.svg b/examples/optics_on_fish_paralog_test_2026-03-10_13-13-45/bootstrap_viz_part1.svg
diff --git a/examples/optics_on_fish_paralog_test_2026-03-10_13-13-45/fig_tree_color_annotation.txt b/examples/optics_on_fish_paralog_test_2026-03-10_13-13-45/fig_tree_color_annotation.txt
@@ -0,0 +1,3 @@
+Name	!color
+C_phantasticus_LWS1	#b3ff00
+C_phantasticus_LWS2	#1eff00
diff --git a/examples/optics_on_fish_paralog_test_2026-03-10_13-13-45/fish_paralog_test_predictions.tsv b/examples/optics_on_fish_paralog_test_2026-03-10_13-13-45/fish_paralog_test_predictions.tsv
@@ -0,0 +1,3 @@
+Names	Single_Prediction	Prediction_Means	Prediction_Medians	Prediction_Lower_Bounds	Prediction_Upper_Bounds	Std_Deviation	%Identity_Nearest_VPOD_Sequence	Sequence_Length	Lmax_Hex_Color
+C_phantasticus_LWS1	556.6	555.0	555.0	549.4	560.2	2.9	85.794	359	#b3ff00
+C_phantasticus_LWS2	522.4	514.9	515.3	500.1	529.1	8.8	79.251	354	#1eff00

diff --git a/...ics_on_fish_paralog_test_2026-03-10_13-13-45/fish_paralog_test_predictions_for_excel.xlsx b/...ics_on_fish_paralog_test_2026-03-10_13-13-45/fish_paralog_test_predictions_for_excel.xlsx
diff --git a/examples/optics_on_fish_paralog_test_2026-03-10_13-13-45/itol_color_annotation.txt b/examples/optics_on_fish_paralog_test_2026-03-10_13-13-45/itol_color_annotation.txt
@@ -0,0 +1,5 @@
+TREE_COLORS
+SEPARATOR TAB
+DATA
+C_phantasticus_LWS1	label_background	#b3ff00
+C_phantasticus_LWS2	label_background	#1eff00
diff --git a/examples/optics_on_optics_results_2026-01-26_15-46-29/arg_log.txt b/examples/optics_on_optics_results_2026-01-26_15-46-29/arg_log.txt
@@ -0,0 +1,17 @@
+Selected Options...
+input_sequence: D:/safra/Github/optics/examples/optics_ex_short.fasta
+report_dir: D:/safra/Github/optics/examples/optics_on_optics_results_2026-01-26_15-46-29
+output_file: optics_results
+model: whole-dataset-mnm
+encoding_method: aa_prop
+tolerate_non_standard_aa: True
+tolerate_incomplete_seqs: False
+blastp: True
+	blastp_report: blastp_report.txt
+	refseq: bovine
+	custom_ref_file: None
+bootstrap: True
+	visualize_bootstrap: True
+		bootstrap_viz_file: bootstrap_viz
+		save_as: svg
+		full_spectrum_xaxis: False
diff --git a/examples/optics_on_optics_results_2026-01-26_15-46-29/blastp_report.csv b/examples/optics_on_optics_results_2026-01-26_15-46-29/blastp_report.csv
@@ -0,0 +1,6 @@
+query_id,status,closest_match_id,match_species,match_opsin_family,match_accession,match_lambda_max,percent_identity,alignment_length,mismatches,gap_opens,e_value,differences_from_match
+Bombus_impatiens|347,Success,MNM1655,Bombus_ impatiens,"opsin, ultraviolet-sensitive [Bombus impatiens]",NP_001267052.1,352.0,100.0,371,0,0,0.0,No Differences
+Bombus_impatiens|424,Success,S801,Apis_cerana,,AB355817,430.0,87.302,378,47,1,0.0,E3K; H13Y; G23A; I25P; Y30H; W35F; F39L; V52L; P67S; A71P; M100I; A112V; A114S; S125A; F178Y; L183F; E194D; Q196E; M205T; S206C; T217I; V220I; Y221L; Q225R; Q228N; R235K; V246A; L248V; M273L; A276V; F277Y; I286V; L293V; H335S; S337A; A338T; V340A; S347T
+Bombus_impatiens|539,Success,MNM1706,Apis_mellifera,,U26026,529.0,88.889,378,40,2,0.0,S3A; A4V; L5S; A14N; H33N; F37Y; L49M; I53V; D83N; T149S; L155I; L158I; G159A; I166G; S193N; D197G; I198L; V199L; V201A; I204L; L205V; L206C; S208G; F214V; W221Y; Y225F; W273F; S277N; Y287F; A328S; P329-; T330S; T334V; V337T
+Neogonodactylus_oerstedii|383,Success,MNM1565,Neogonodactylus_oerstedii,SWS/UVS,STO|Neoer|UVS|AIF73508,383.0,100.0,368,0,0,0.0,A348-
+Neogonodactylus_oerstedii|334,Success,MNM1700,Neogonodactylus_oerstedii,SWS/UVS,STO|Neoer|UVS|AIF73507,388.0,100.0,349,0,0,0.0,No Differences