diff --git a/education/HADDOCK24/HADDOCK24-antibody-antigen-basic/index.md b/education/HADDOCK24/HADDOCK24-antibody-antigen-basic/index.md index 5d4140d5..b47dcd84 100644 --- a/education/HADDOCK24/HADDOCK24-antibody-antigen-basic/index.md +++ b/education/HADDOCK24/HADDOCK24-antibody-antigen-basic/index.md @@ -433,6 +433,15 @@ align cluster5_1 and chain A, 4G6M-matched and chain A, cycles=0
rms_cur cluster5_1 and chain B, 4G6M-matched
+**Note:** On some machines the pymol rms_cur command can fail due to a bug in the PyMOL software. In this case you can use the following command instead: + + +align cluster1_1, 1GGR, cycles=0 + + +This will align the two structures based on the all-atom RMSD, different from the ligand-RMSD (l-RMSD) that you can calculate with rms_cur and the above commands. + + Repeat the align and rms commands for each cluster representative and take note of the reported RMSD value.