Hi Elaine and Eric, 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 close session On Fri, Dec 8, 2023 at 8:41 PM Ellen Shrock <eshrock2023@gmail.com> wrote:
Thank you, Eric!
Best, Ellen
On Fri, Dec 8, 2023 at 4:54 PM Eric Pettersen <pett@cgl.ucsf.edu> wrote:
On Dec 7, 2023, at 7:16 PM, Ellen Shrock via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
for res in list(chimera.selection.residues):
This should be:
from chimera.selection import currentResidues for res in currententResidues():
There is no easy way to get the findclash command to append to a file. You would have to open the file yourself, call the underlying findclash Python function, parse the results and format it into the output file. Probably easier to just concatenate the files afterward with the Unix 'cat' command.
--Eric
Eric Pettersen UCSF Computer Graphics Lab