diff --git a/education/HADDOCK24/HADDOCK24-protein-protein-basic/index.md b/education/HADDOCK24/HADDOCK24-protein-protein-basic/index.md index 17886c4a7..f6686864e 100644 --- a/education/HADDOCK24/HADDOCK24-protein-protein-basic/index.md +++ b/education/HADDOCK24/HADDOCK24-protein-protein-basic/index.md @@ -105,6 +105,9 @@ Try to locate the histidines in this structure. Is there any phosphate group present in this structure? +*Hint* : you can select phosphate atoms with the following PyMOL command: +select elem P + Note that you can zoom on the histidines by typing in PyMOL: zoom resn HIS @@ -506,6 +509,14 @@ In the blind protein-protein prediction experiment [CAPRI](https://capri.ebi.ac. rms_cur cluster1_1 and chain B, 1GGR
+**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. + In CAPRI, the l-RMSD value defines the quality of a model: * acceptable model: l-RMSD<10Å