Hi Brenton,
you can find a detailed documentation for the Jmol scripting language at the
following URL : http://chemapps.stolaf.edu/jmol/docs/
Regarding your question, when you start Jmol, you open up the Jmol console (for
example by right-clicking the visualization area).
When you are all set, you can type in your scripts.
First define your selection (by defaults all atoms are selected and the ensuing
commands would affect the whole macromolecule), then choose your display and
colouring schemes.
E.g. :
select protein;
ribbon only; //or cartoon only or rocket only depending on your preferences
color structure;
select ligand;
spacefill;
color cpk;
hide (cd, so4);
and you're done ! (I don't know what you'd want to do with the water molecules
displayed ; you can select those with any of the following keywords : "water",
"hoh", "solvent")
Happy Jmoling,
Paul
Le 01/01/15 22:40, Brenton Horne <brentonho...@ymail.com> a écrit :
>
> Hi,
>
> My question is basically the title of this email (How do I display my
> macromolecule in ribbons style and my ligands in ball-and-stick style?),
> but I'd also like to be able to adjust the colour of the ribbons to
> secondary type and I'd like the ligands coloured CPK. It'd be fantastic
> if I could choose which ligands I want to display and which I'd like to
> hide. If you'd like to show me how to do this with an example (which I
> think will be sufficient here) here are some parameters for the example
> I'm working on atm:
>
> PDB ID: 3EIG
>
> Ligand IDs: CD, MTX, SO4.
> I'd like to display just MTX.
>
> Thanks for your time,
> Brenton
>
>
>
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