It appears that if atoms are not in one frame they can't be considered in
Hbonding despite the fact of selecting them all, unless i missed something.
First example doesn't work, since I've done something simmilar. Second
example works as expected but it's not a solution for me since I'd like to
preview few conformations at one time.
Actually I'm setting protein with "set backgroundModel 1.1;" which
is convenient since you can jump easily between ligands. Maybe then Jmol
should be more flexible when user wants to compute hbonds explicitly
between two frames/models?
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
[email protected]
2012/6/18 Angel Herráez <[email protected]>
> 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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