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