Devprev; Rama Map; collected comments

Case number:954892-2002190
Topic:Developer Preview
Opened by:Bletchley Park
Status:Open
Type:DevPrev Issue
Opened on:Friday, March 18, 2016 - 20:44
Last modified:Sunday, January 5, 2020 - 11:17

#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.

(Fri, 03/18/2016 - 20:44  |  15 comments)


jflat06's picture
User offline. Last seen 2 hours 38 min ago. Offline
Joined: 09/29/2010
Groups: Window Group

I did not design the tool, but for #3, can you try putting the cutpoint a couple residues away?

Joined: 05/19/2009
Groups: Contenders

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.

spvincent's picture
User offline. Last seen 14 hours 12 min ago. Offline
Joined: 12/07/2007
Groups: Contenders

#4 Is the Ideal Loop for information only or is there some mechanism for incorporating them into an existing structure (like remix)?

Joined: 05/19/2009
Groups: Contenders

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.

Joined: 09/24/2012
Groups: Go Science

#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)

jeff101's picture
User offline. Last seen 4 hours 3 min ago. Offline
Joined: 04/20/2012
Groups: Go Science

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!

jeff101's picture
User offline. Last seen 4 hours 3 min ago. Offline
Joined: 04/20/2012
Groups: Go Science

(6.1) At 8:39 in Susume's Rama Map #2 - Copying a Loop
video (https://www.youtube.com/watch?v=o4ZOY8MBG9g),
the 3D view of the protein is colored using the
ABEGO color scheme. I see red, blue, green, and
yellow regions there, as if each residue has its
dihedral angles in its amino acid's preferred
region of the Rama Map. What color is used in the
ABEGO color scheme for a residue with dihedral
angles outside its amino acid's preferred region,
where the Rama Map will be white? I think there
should be a 5th color (not red, blue, green, or
yellow) on these residues in the 3D view of the
protein.

Also at 8:39, the Rama Map shown has 2 points along
the x axis and 1 point along the y axis. One of the
points along the x axis should be one end of the
protein, and the point along the y axis should be the
other end of the protein. The 3D view of the protein
has a yellow triangle at one end (the top of the
left-most strand) and a red triangle at the other end
(the top of the 2nd strand from the right). Do these
colors make sense compared to where these residues
appear on the Rama Map?

These questions are related to (6) above because if a
5th color is used in the ABEGO color scheme, one can
quickly tell which residues of the protein have dihedral
angles outside their amino acids' preferred regions
(just look for the residues with this 5th color in the
3D view of the protein).

jeff101's picture
User offline. Last seen 4 hours 3 min ago. Offline
Joined: 04/20/2012
Groups: Go Science

The image below is from Susume's Rama Map #2 - Copying a Loop
video at 8:39 (https://www.youtube.com/watch?v=o4ZOY8MBG9g)

jeff101's picture
User offline. Last seen 4 hours 3 min ago. Offline
Joined: 04/20/2012
Groups: Go Science

(7.1) When one hovers over a residue on the Rama Map,
could you list its dihedral angle values?

jeff101's picture
User offline. Last seen 4 hours 3 min ago. Offline
Joined: 04/20/2012
Groups: Go Science

(8.1) In lieu of commands like GetPhiPsi and SetPhiPsi that read or set the dihedral angles to particular values, it would be useful to have a way to reset the dihedral angles for a large group of residues to the same values. Then players could easily make any of the 3 linear groups (p.21 fig.8) or 5-10 main regions of the Rama Map (p.10) discussed on pp.6-8,10-11,21 of https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061398/ and cited by Susume at http://fold.it/portal/node/2002349

Manually, one could select a large group of points (residues) on the Rama Map and then drag them all simultaneously to a single point on the Rama Map. In LUA, there could be a command like CopyPhiPsi(goal_res,selected_res) that would copy the dihedral angles from residue number goal_res to all the residue numbers in the array selected_res.

These copy functions would make life easier for players without giving us access to the numerical values of the dihedral angles.

jeff101's picture
User offline. Last seen 4 hours 3 min ago. Offline
Joined: 04/20/2012
Groups: Go Science

(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!

Susume's picture
User offline. Last seen 10 hours 13 min ago. Offline
Joined: 10/02/2011

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.

Joined: 04/24/2014
Groups: None

> There are also some suggestions in the comments to the rama map blog post: http://fold.it/portal/node/2002173

It would also help the developers and scientists if we could (in future feature updates) give a try and keep the suggestions in the same thread*, so that they are less likely to get lost and easier to track for the team. :)

* and bugs in feedback

Joined: 09/24/2012
Groups: Go Science

bump,

Actually, it would be great to see all 1-10 suggestions implemented.

The most I would personally use are 6 and 10 but all would be great.

jeff101's picture
User offline. Last seen 4 hours 3 min ago. Offline
Joined: 04/20/2012
Groups: Go Science

Bump. Suggestion (8.1) above would come in handy in the poly-proline puzzles.
Earlier today I tried to make a bunch of extra proline residues have dots
in the Rama Map where the poly-proline helix's dots lie. In the end, I
dragged these dots one by one into the desired spot on the Rama Map. It
would have been nice if I could have selected all these proline residues
using the Selection Interface and then dragged all of their Rama Map dots
into the desired spot simultaneously.

Sitemap

Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons