More usability comments

Some more comments…

(1) Icon for Rotation Tool too ambiguous. Why not an arrow in a circle?
(2) Impossible to make tools icons in a list of icons of width 1 or
move them onto the tool bar. They currently take up too much space.
(3) Tools menu contains different content than icons in Tools toolbar!
(4) What on earth is an engine? I don’t think valuable screen estate
needs to be devoted to permanent information on Engines and Engine
configuration.
(5) Manipulation Tool - dragging a single unconnected (water) atom in
protein 1abe.pdb takes about a second. That is, a second after I stop
dragging the atom, the atom disappears from its original location and
moves to the correct location.
(6) What does selecting an atom do? I’ve selected it. It turned blue.
Then I click on Stick. And everything changes to Stick, not just the
atom I’ve selected.
(7) I turn Label on/off…nothing happens although I expected atoms to
become labelled with their element symbol…
(8) To crash Avogadro, open 1abe.pdb. Click on Van-der-Waals Sphere
(no need to turn them on). Click Primitives. Change the minus into a
plus for Atoms. Change the plus into a minus for Atoms. Bye bye
Avogadro…
(9) When in Manipulation Tool, it should be possible to quickly switch
into rotate mode because you can only drag an atom in the plane of the
screen (right?). If I don’t click on an atom it should rotate around
the last atom I clicked. Something like that.
(10) Manipulation Tools. Middle button. I couldn’t figure out how it
worked. As soon as you start drag in any direction it makes the atom
’bigger’ with a selection halo, but then the atom slows gets smaller
(i.e. further away). How to make it bigger? Why not include a clipping
plane so I know when the atom is at the right distance?
(11) Rotation tool - Why not just rotate around the centroid of the
atoms on the screen, rather than all atoms? Who would want to do the
latter?
(12) Bond centric manipulation tool. If I choose a bond, and then
click and drag in empty space, it should rotate around the bond,
instead of around the centroid of the molecule. The latter just
rotates my bond out of the screen…

I know you would prefer me to file bug reports or feature requests in
the SF trackers, but the barrier is too high for this number of
issues. With time, I will file any unaddressed issues…

Regards,
Noel

Hi Noel,

Thanks for the reports.

Perhaps you saw that i addressed the issue you reported about the
"big bubble on zoom".

(7) I turn Label on/off…nothing happens although I expected atoms to
become labelled with their element symbol…

That’s indeed what should have happened. I don’t know why it didn’t work
for you. We have some occlusion issues, but at least with “balls and
sticks” engine, the text shows correctly.

(11) Rotation tool - Why not just rotate around the centroid of the
atoms on the screen, rather than all atoms? Who would want to do the
latter?

That is a very good idea. Thanks for it. I don’t have any time currently
and am leaving for a conference but I’ll at least explain how this can be
quite easily achieved using our framework. Maybe you, or another
developer, can then actually write the code.

The Camera::project() function allows to get the 2d window coordinate of
an atom. This can be used to determine whether or not a given atom is on
screen.

A faster, approximative approach is to do as we currently do our frustum
culling: compute the dot product of the Camera-Atom vector with the
"Looking forward" vector.

Using either method to determine whether a given atom is on screen, one
can then do something like this pseudocode:

int atoms_of_screen = 0;
Eigen::Vector3d center_atoms_on_screen(0,0,0);
foreach(atom, all_atoms_in_molecule)
{
if(is_on_screen(atom))
{
atoms_of_screen++;
center_atoms_on_screen += atom.pos();
}
}
center_atoms_on_screen /= atoms_of_screen;

Cheers,

Benoit

(1) Icon for Rotation Tool too ambiguous. Why not an arrow in a
circle?
(2) Impossible to make tools icons in a list of icons of width 1 or
move them onto the tool bar. They currently take up too much space.

Honestly, I’d like new, and larger size icons for the tools. As for
screen space, Marcus (cryos) already posted about saving the position
of tool windows.

I’d also like to move some of the tool windows (e.g., render engine
configuration) into a menu item. I just need to work out a "wrapper"
window.

(3) Tools menu contains different content than icons in Tools toolbar!

The Tools menu totally needs to change. It’s really a list of
"extensions," so the name is horribly confusing. I’d like to separate
it into “Build” and “Compute” and “Select” for now. I think that
solves many possible extensions for a while.

(4) What on earth is an engine? I don’t think valuable screen estate
needs to be devoted to permanent information on Engines and Engine
configuration.

See above. Engines are rendering classes.

(6) What does selecting an atom do? I’ve selected it. It turned blue.
Then I click on Stick. And everything changes to Stick, not just the
atom I’ve selected.

Right now, the engines don’t respect selection. It’s a royal pain to
set up a few atoms to render with one engine and not with another.
It’s possible, but it’s hardly user-friendly.

What does select do? Try selecting a few atoms, then copy/paste. Try
selecting a few atoms, then use the manipulate tool. Try selecting a
few atoms and then “add hydrogens.” Try selecting some atoms and then
"Clear."

Try dragging a rectangular rubber band with the select tool.

All this goes to say that we need some screen cast tutorials.

plus for Atoms. Change the plus into a minus for Atoms. Bye bye
Avogadro…

Do you think you could get a stack backtrace and file this one as a
bug? Clearly we don’t want crashes.

(9) When in Manipulation Tool, it should be possible to quickly switch
into rotate mode because you can only drag an atom in the plane of the
screen (right?).

You can quickly switch tools with the function keys. There are
shortcuts for each tool, actually. I also usually use the manipulate
tool’s own rotate function with a set of selected atoms.

Thanks for the feedback, it’s all welcome. (It’d be really nice if
you’d file bug reports, even if it’s 12 of them – you could have just
filed the bugs rather than typing out the email which probably took
the same amount of time.)

Cheers,
-Geoff