#01. Zoom in Rama map top window works opposite from zoom in normal window. Shift-mouse away zooms in instead of out, like in the normal interface.
#02. Slecting something in Rama map does not show the residu as slected in original interface, it would be useful to see it selected somehow.
#03. moving the dot in the map does indeed rotate things in the normal window, however, it will wreck a design. How is one to use the moving dot interface constructively ? I can imagine using cutpoints to isolate the selected Rama point in the main window so I can rotate it into a proper position, bur the cutpoints will move the dot in the Rama map. If I then move the dot in the Rama map and then close the cutpoints the dot in the Rama map is back where it started. Not very useful I think ?
#04. Showing the residu number only when hovering is a bit odd, why not show it always especially when the dot is selected ?
When adding comments (new points) to this thread, please give them a new item number so later posts can reference them more easily.
I did not design the tool, but for #3, can you try putting the cutpoint a couple residues away?
re #03 suggestion: it does not produce a more statisfying result with me. The dot moves around as soon as you open or close cutpoints, even if those cutpoints are a bit further away.
#4 Is the Ideal Loop for information only or is there some mechanism for incorporating them into an existing structure (like remix)?
Thanks for that question spvincent. 'Ideal Loop for information only' will then be item #05. I purposely add the # and 0 so searching the page will be easier later on.
#2.1 and showing on Rama map, the residue that is displayed with tab in original interface
#5 No limit to size reduction of the rama Map (it's still too big on a small laptop screen)
I enjoyed Susume's Rama Map videos at
http://fold.it/portal/node/2002398
and have some suggestions/ideas based on them:
(6) On Rama Maps, it seems like the white box is for the
selected residue while the black boxes are for the rest
of the residues. Is it possible to have a 3rd shade or a
different shape (star, triangle, etc.) for each residue with
dihedral angles outside their amino acid's preferred range?
Then we could check the whole protein without having to flip
through Rama Maps for each residue.
(7) I like that one can select & drag residues on the Rama Map
to change their dihedral angles. Would it be possible to list
in the corner of the map the selected residue's dihedral angle
values and update this listing as one drags the residue around?
Would it be possible to have an input box where one can type
the desired values for the dihedral angles?
(8) Would it be possible to make LUA commands like GetPhi,
GetPsi, SetPhi, and SetPsi to read and set the dihedral angles
for selected residues?
Thanks!
(7.1) When one hovers over a residue on the Rama Map,
could you list its dihedral angle values?
(9) In the information box brought up when one Tabs on a residue
(the one listing all the energy values for that residue),
could you also list the dihedral angles for that residue?
Thanks again!
There are also some suggestions in the comments to the rama map blog post: http://fold.it/portal/node/2002173
(10) It would be really helpful if the angles of the suggested ideal loops could be given to us in a way that we can readily copy (something better than just eyeballing the tiny samples). This could be putting their dots on the rama map so we can drag and drop our dots onto them, or showing us the angles as numbers when we hover over the thumbnail, and showing us the angles of our own residues in one or more of the ways jeff has suggested.
