Thank you Ángel for your research. This works. I can show my students
that hbonds feature works in the pop-up menu with pdb files and if they
use mol2 files, it can be done via console.
I think we continue with mol2 format because of the partial charge data
and electrostatic potential surfaces included in mol2. We also need the
multi frame feature at the course.
Best regards
Johannes
28.1.2012 13:51, Herráez Sánchez Ángel kirjoitti:
Well, I have done a little research and yes, I can confirm Johannes'
observation.
Jmol 12.2.2 has also disabled the popup menu "calculate Hbonds" for MOL2 files,
but not for PDB files. However, the ability to calculate is there in the script console.
These "feature" is by design, since that popup menu subentry is in the source
code part of a group being active only on PDB files.
I am not sure is this can/should be overruled or what is the sensible solution
in coding terms.
Other options like "select> protein" etc. shpuld also be disabled, right? That
is because formats other than PDB are not prepared to provide the necessary information.
Could you get away from mol2 format? Maybe convert to pdb?
Another possible way may be to build a custom menu
http://wiki.jmol.org/index.php/Custom_Menus
where you will add an option linked to the "hbonds calculate" script.
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