I hope all is well. I am writing because I am using the chimerax command 'label sel residues height 1' but I noticed that the insertion codes are not making it into the labels. I attached an example cxc session along with the commands provided. In, for example, model #4, there are two residues labeled '100' even though when I hover over the residues, they have insertion codes. Do you know if there is a way I can label the residues with the position numbers including the insertion codes?

(I copied below the entire script I ran. Please let me know if there is any additional information I can provide.)

Thanks,

Ellen

# Directory: E_antigen_Y_33_heavy_len54
# Subdirectory: Y_33_heavy_and_Y_52_heavy_len9
# Directory: R_antigen_D_50_light_len73
# Subdirectory: D_50_light_and_W_32_light_and_Y_91_light_len9
open /home/eshrock/Projects/eshrock_scratch_2024_02_28/antibody/2024_01_25_removing_Abs_similar_to_RBD_and_retraining_RF2_and_RFab/2024_02_29_pred_CoVAbDab_with_DMS_hotspots_using_retrained_models/predictions_for_all_Abs_with_and_without_DMS_hotspots/RFab_pred_using_corrected_models_actually_no_CoV_Ab_ag/model1/with_hotspots/renumbered_anarci/2087_BD56-1843_pdb6w41_C_T_coordinates.json_best_anarci_chothia_T_renumbered_HLT.pdb
open /home/eshrock/Projects/eshrock_scratch_2024_02_28/antibody/2024_01_25_removing_Abs_similar_to_RBD_and_retraining_RF2_and_RFab/2024_02_29_pred_CoVAbDab_with_DMS_hotspots_using_retrained_models/predictions_for_all_Abs_with_and_without_DMS_hotspots/RFab_pred_using_corrected_models_actually_no_CoV_Ab_ag/model1/with_hotspots/renumbered_anarci/2104_BD56-1862_pdb6m17_E_T_coordinates.json_best_anarci_chothia_T_renumbered_HLT.pdb
open /home/eshrock/Projects/eshrock_scratch_2024_02_28/antibody/2023_12_22_analysis_for_CoVAbDab_GRAB_paper/AF3_predictions_CoV2/unzipped_AF3_pred_from_Max/WTRBD/fold_bd56_534_wtrbd_unzipped/fold_bd56_534_wtrbd_model_0_anarci_chothia_T_renumbered_HLT.pdb
open /home/eshrock/Projects/eshrock_scratch_2024_02_28/antibody/2023_12_22_analysis_for_CoVAbDab_GRAB_paper/AF3_predictions_CoV2/unzipped_AF3_pred_from_Max/WTRBD/fold_bd_824_wtrbd_unzipped/fold_bd_824_wtrbd_model_2_anarci_chothia_T_renumbered_HLT.pdb
open /home/eshrock/Projects/eshrock_scratch_2024_02_28/antibody/2023_12_22_analysis_for_CoVAbDab_GRAB_paper/AF3_predictions_CoV2/unzipped_AF3_pred_from_Max/WTRBD/fold_bd56_1908_wtrbd_unzipped/fold_bd56_1908_wtrbd_model_1_anarci_chothia_T_renumbered_HLT.pdb
matchmaker #1/T to #5/C pairing ss
matchmaker #2/T to #5/C pairing ss
matchmaker #3/C to #5/C pairing ss
matchmaker #4/C to #5/C pairing ss
set bgColor white
hbonds #1/T:346 color #000000 restrict #1/H #1/L
hbonds #2/T:346 color #000000 restrict #2/H #2/L
hbonds #3/C:346 color #000000 restrict #3/A #3/B
hbonds #4/C:346 color #000000 restrict #4/A #4/B
hbonds #5/C:346 color #000000 restrict #5/A #5/B
select #1/H #2/H #3/A #4/A #5/A
color sel #ffff001f
select #1/L #2/L #3/B #4/B #5/B
color sel #00ffff1f
select #1/T #2/T #3/C #4/C #5/C
color sel #ff00ff1f
select #1/T:346 #2/T:346 #3/C:346 #4/C:346 #5/C:346
label sel residues height 1
color sel #ff00ffff
show sel atoms
select #1/L:50
color sel #00ffffff
show sel atoms
label sel residues height 1
select #1/H:100C
color sel #ffff00ff
show sel atoms
label sel residues height 1
select #1/H:100D
color sel #ffff00ff
show sel atoms
label sel residues height 1
select #1/H:100E
color sel #ffff00ff
show sel atoms
label sel residues height 1
select #1/L:32
color sel #00ffffff
show sel atoms
label sel residues height 1
select #1/L:91
color sel #00ffffff
show sel atoms
label sel residues height 1
select #2/L:50
color sel #00ffffff
show sel atoms
label sel residues height 1
select #2/H:100A
color sel #ffff00ff
show sel atoms
label sel residues height 1
select #2/L:32
color sel #00ffffff
show sel atoms
label sel residues height 1
select #2/L:91
color sel #00ffffff
show sel atoms
label sel residues height 1
select #3/A:100B
color sel #ffff00ff
show sel atoms
label sel residues height 1
select #3/B:50
color sel #00ffffff
show sel atoms
label sel residues height 1
select #3/B:32
color sel #00ffffff
show sel atoms
label sel residues height 1
select #3/A:100C
color sel #ffff00ff
show sel atoms
label sel residues height 1
select #3/B:91
color sel #00ffffff
show sel atoms
label sel residues height 1
select #4/A:100A
color sel #ffff00ff
show sel atoms
label sel residues height 1
select #4/B:50
color sel #00ffffff
show sel atoms
label sel residues height 1
select #4/B:32
color sel #00ffffff
show sel atoms
label sel residues height 1
select #4/A:99
color sel #ffff00ff
show sel atoms
label sel residues height 1
select #4/A:100B
color sel #ffff00ff
show sel atoms
label sel residues height 1
select #4/B:91
color sel #00ffffff
show sel atoms
label sel residues height 1
select #5/A:100
color sel #ffff00ff
show sel atoms
label sel residues height 1
select #5/B:50
color sel #00ffffff
show sel atoms
label sel residues height 1
select #5/B:32
color sel #00ffffff
show sel atoms
label sel residues height 1
select #5/B:91
color sel #00ffffff
show sel atoms
label sel residues height 1
sel
color sel byhetero
hide H
select clear
save /home/eshrock/Projects/eshrock_scratch_2024_02_28/antibody/2023_12_22_analysis_for_CoVAbDab_GRAB_paper/2024_07_24_GRAB_analysis/WT_filtered_SC_hotspot_contacts_mult_contexts_GRAB/chimerax_images/R_D_50_light_and_W_32_light_and_Y_91_light_len9_IGKV1-5_cluster_16.cxs
save /home/eshrock/Projects/eshrock_scratch_2024_02_28/antibody/2023_12_22_analysis_for_CoVAbDab_GRAB_paper/2024_07_24_GRAB_analysis/WT_filtered_SC_hotspot_contacts_mult_contexts_GRAB/chimerax_images/R_D_50_light_and_W_32_light_and_Y_91_light_len9_IGKV1-5_cluster_16.png width 859 height 785 supersample 3