[Jmol-users] RE: loading 2 structures at once

[Miguel <mi...@jm...>]

Dave wrote:
> I am writing to inquire whether it is possible to load two structures at
> once into the Jmol applet.

Well, yes and no ... probably more 'no' than 'yes'.

Jmol can currently only 'load' one molecular model file at a time.

But, there are some file formats that support more than one 'model' within
a single file. For example, .xyz, .pdb, .cif, .cml ...

So, if you can put two molecular models in the same file, then Jmol will
load them up. You can then switch between models by saying 'frame 1' or
'frame 2'. Alternatively, you can say 'frame all' to display all models at
the same time. Then use 'restrict' to shut down the things you do not want
to see.

Note that this does not allow you to translsate/zoom/rotate the individual
models independently. (I hope to add this type of 'layer' support for
multiple molecular model files, each independently controllable, at some
point in the future.)

> I want to do this to be able to display molecular models/x-ray
> structures of
> compounds bound/docked into active sites of proteins. This will be
> integrated in with the other data and provide a very useful tool for our
> scientists. I envision loading a protein/active site and then having the
> user choose various ligands that have been docked into it.

I understand that you want to show things in the 'docked state' ... as
opposed to showing a movie of the 'docking process'.

Since you are working with proteins, you will want to use .pdb or .cif files.

I think what you want is your base protein as one model, then your
accessories (ligands?) as other models. You can then turn on the
accessories independently.

Alternatively, you could have the naked protein as one model, then the
various accessorized versions of the protein as other models.

In either case you need to position/scale/align things so that things look
correct when you add in additional models (or switch between models).
Unfortunately, I have no idea what tools one can use to build such things
and rotate the coordinates so that they are aligned properly.

Good luck.


Miguel