Hello Maciek
I am not certain, but I think that you probably cannot get Jmol
looking for bonds between models. After all, atoms and bonds belong
to a model, they cannot be cross-model.
I'd suggest two possible workarounds:
#1 (probably will not work) Make all models visible before you try:
frame all;
select *;
calculate hBonds;
#2 load the ligand file into the same model/frame:
load "protein.pdb";
set appendNew false;
load append "ligand.pdb";
select *;
calculate hBonds;
Quoting from hte documentation:
If set appendNew false has been issued and only one model is in the
appended file, then the file model is added to the currently
displayed model, creating no additional frames. Starting in Jmol
11.4, multiple files may be appended if the specified file is a ZIP
file.
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