Re: [Jmol-users] Show only protein atoms close to the ligand

[Rolf H. <rh...@fl...>]

Noel O'Boyle wrote:
> I am just starting to use Jmol and I would really appreciate some help...
> 
> I have a protein file, and I have a ligand file. Task 1 is to select
> only those protein atoms within 6Ang of the ligand. Task 2 is to
> display only these selected atoms. Task 3 is to draw the isosurface of
> the selected atoms.
> 
> I just cannot get as far as Task 2. Here's what I've done:
>     load file:///D:/NegativeData/RUNS/dock_inactives_paper/1w2g/protein.mol2
>     load APPEND file:///D:/NegativeData/data/new_set_ccdc/1w2g/ligand.mol
>     select within(6.0, true, */2)
> 
> The last line selects 291 atoms; since there are only 31 atoms in the
> ligand and there are 5840 atoms in the protein it looks like Task 1
> has been accomplished.
> 
> At this point the applet just shows the ligand. If I try "display" it
> just says "0 atoms hidden" and doesn't change anything. Any ideas?
> 

I would expect that you have to add a "frame all" command after loading:

  load ...
  load APPEND ...
  frame all
  select within(6.0, true, */2)
  display selected

If you load several files simultaneously they are accessible as
individual frames. In order to show all frames at once you need the
command "frame all". If you want to show only one specific frame you can
use the command "frame frame_number" (e.g.: frame 1).

But since each file could contain several models, which are also loaded
into individual frames, I think it would be better to use the extended
syntax "frame file_number.model_number" (e.g.: frame 1.1).

The "frame" command is uncoupled from the "display" command. This means
that only if a frame is selected for showing its content with "frame
..." the content of this frame is shown according to the setting made
with "display ...".

Regards,
Rolf