Selecting chain via command line
Hello, I am trying to write a script that will iterate through lists of PDB IDs, the relevant antibody chain labels within those PDBs, and antigen chain labels, and annotate the contacts between the antibody and antigen using the command findclash. After opening each PDB file, I am struggling to find a way to select the antibody chains as "sel1" and the antigen chain(s) as "sel2" since the command "select" does not seem to recognize chain labels. Could you please help me find a way to accomplish my goal? Thank you, Ellen
Hi Ellen, Just about any command that takes a set of atoms will take the chain ID, but there is a specific syntax which may take a little getting used to. Some examples with the "select" command: select :.A select #0:.C The first one selects all chains A (multiple models, if present) and the second one selects chain C but only in model #0. There are more examples in this page about command-line specification: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> ...specifically in this section, see chain examples under "subcategories": <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#hiera...> Say you have structure 2bdn which has antigen chain A with antibody light chain L and heavy chain H (we use the "author" chain IDs), <https://www.rcsb.org/structure/2BDN> ...and you want to find contacts of A with L+H collectively. Your commands could be something like the following, although you may want different options/values. Note that you do not need to make a selection, you can just specify the chains directly in the findclash command. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> open 2bdn findclash :.H:.L test :.A overlap -0.5 hb 0 reveal true log true ....and then look in the Reply Log (under Favorites in menu) to see the details. Or you can use the option to save a text file of the results, see the findclash help link above. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 4, 2023, at 12:55 PM, Ellen Shrock via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hello,
I am trying to write a script that will iterate through lists of PDB IDs, the relevant antibody chain labels within those PDBs, and antigen chain labels, and annotate the contacts between the antibody and antigen using the command findclash.
After opening each PDB file, I am struggling to find a way to select the antibody chains as "sel1" and the antigen chain(s) as "sel2" since the command "select" does not seem to recognize chain labels.
Could you please help me find a way to accomplish my goal?
Thank you, Ellen
Hi Elaine, This was extremely helpful and exactly what I was looking for, thank you! Best, Ellen On Wed, Oct 4, 2023 at 1:22 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Ellen, Just about any command that takes a set of atoms will take the chain ID, but there is a specific syntax which may take a little getting used to. Some examples with the "select" command:
select :.A select #0:.C
The first one selects all chains A (multiple models, if present) and the second one selects chain C but only in model #0. There are more examples in this page about command-line specification:
< https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html
...specifically in this section, see chain examples under "subcategories": < https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#hiera...
Say you have structure 2bdn which has antigen chain A with antibody light chain L and heavy chain H (we use the "author" chain IDs), <https://www.rcsb.org/structure/2BDN>
...and you want to find contacts of A with L+H collectively. Your commands could be something like the following, although you may want different options/values. Note that you do not need to make a selection, you can just specify the chains directly in the findclash command. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
open 2bdn findclash :.H:.L test :.A overlap -0.5 hb 0 reveal true log true
....and then look in the Reply Log (under Favorites in menu) to see the details. Or you can use the option to save a text file of the results, see the findclash help link above.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 4, 2023, at 12:55 PM, Ellen Shrock via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Hello,
I am trying to write a script that will iterate through lists of PDB IDs, the relevant antibody chain labels within those PDBs, and antigen chain labels, and annotate the contacts between the antibody and antigen using the command findclash.
After opening each PDB file, I am struggling to find a way to select the antibody chains as "sel1" and the antigen chain(s) as "sel2" since the command "select" does not seem to recognize chain labels.
Could you please help me find a way to accomplish my goal?
Thank you, Ellen
Hi Elaine, I hope all is well. Previously you helped me iterate through lists of pdb files, annotate the contacts between the antibody and antigen using the command findclash. Now, I was hoping to iterate over each residue of the antigen (in this case labeled as chain T) and identify all antibody residues that contact that particular antigen residue. I have copied my script below, but the iteration over the residues isn't working. I was wondering if you could help me with this? Also, do you know if there is a way to append to a file for each pdb instead of saving a different file for each residue in my case? Thanks a lot, Ellen import chimera import os from chimera import runCommand as rc # use 'rc' as shorthand for runCommand from chimera import replyobj # for emitting status messages from chimera.tkgui import saveReplyLog from chimera import selection # change to folder with data files os.chdir("/home/eshrock/scratch/") out_path = '/home/eshrock/scratch/findclash_results/' # gather the names of .pdb files in the folder file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] # loop through the files, opening, processing, and closing each in turn for fn in file_names: replyobj.status("Processing " + fn) # show what file we're working on rc("open " + fn) rc("select :.T") for res in list(chimera.selection.residues): save_file_name = out_path + fn + "_" + res +'_findclash.txt' rc("findclash :.H:.L test " + res + " overlapCutoff -1.0 hbondAllowance 0 namingStyle simple saveFile " + save_file_name) rc("close all") rc("stop now") On Wed, Oct 4, 2023 at 1:26 PM Ellen Shrock <eshrock2023@gmail.com> wrote:
Hi Elaine,
This was extremely helpful and exactly what I was looking for, thank you!
Best, Ellen
On Wed, Oct 4, 2023 at 1:22 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Ellen, Just about any command that takes a set of atoms will take the chain ID, but there is a specific syntax which may take a little getting used to. Some examples with the "select" command:
select :.A select #0:.C
The first one selects all chains A (multiple models, if present) and the second one selects chain C but only in model #0. There are more examples in this page about command-line specification:
< https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html
...specifically in this section, see chain examples under "subcategories": < https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#hiera...
Say you have structure 2bdn which has antigen chain A with antibody light chain L and heavy chain H (we use the "author" chain IDs), <https://www.rcsb.org/structure/2BDN>
...and you want to find contacts of A with L+H collectively. Your commands could be something like the following, although you may want different options/values. Note that you do not need to make a selection, you can just specify the chains directly in the findclash command. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
open 2bdn findclash :.H:.L test :.A overlap -0.5 hb 0 reveal true log true
....and then look in the Reply Log (under Favorites in menu) to see the details. Or you can use the option to save a text file of the results, see the findclash help link above.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 4, 2023, at 12:55 PM, Ellen Shrock via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Hello,
I am trying to write a script that will iterate through lists of PDB IDs, the relevant antibody chain labels within those PDBs, and antigen chain labels, and annotate the contacts between the antibody and antigen using the command findclash.
After opening each PDB file, I am struggling to find a way to select the antibody chains as "sel1" and the antigen chain(s) as "sel2" since the command "select" does not seem to recognize chain labels.
Could you please help me find a way to accomplish my goal?
Thank you, Ellen
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
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
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
Hi Ellen, You sent this question to the Chimera address -- in the future, please send ChimeraX questions to the ChimeraX address chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> CC'd here to avoid confusing the other users. This answer is for ChimeraX: It works for me: labels show the insertion code. Make sure you have ChimeraX 1.8 or newer. Example 1h4w which has residues with insertion codes 184A, 188A, 221A: open 1h4w label :184,184A height 2 I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 17, 2024, at 10:20 PM, Ellen Shrock via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
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
Hi Elaine, Sorry, I'll keep the proper email addresses in mind. Updating to 1.8 fixed it, thank you!! Best, Ellen On Wed, Sep 18, 2024 at 8:31 AM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Ellen, You sent this question to the Chimera address -- in the future, please send ChimeraX questions to the ChimeraX address chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> CC'd here to avoid confusing the other users.
This answer is for ChimeraX:
It works for me: labels show the insertion code. Make sure you have ChimeraX 1.8 or newer. Example 1h4w which has residues with insertion codes 184A, 188A, 221A:
open 1h4w label :184,184A height 2
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 17, 2024, at 10:20 PM, Ellen Shrock via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
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
participants (3)
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Elaine Meng -
Ellen Shrock -
Eric Pettersen