Opened 3 years ago

Closed 3 years ago

#7066 closed enhancement (fixed)

Douse tool enhancements

Reported by: Eric Pettersen Owned by: Eric Pettersen
Priority: high Milestone:
Component: Structure Editing Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

  • Default representation for 7rtb is sphere. To best see the environment of the water, it might be useful to set the default view as "stick". Otherwise, the user will have to manually change the representation.
  • After deleting a water, the view zooms out and all waters in the list are highlighted in blue. Ideally, the view would go to the next water in the list? Otherwise, the user has to keep track of where they were.
  • I wonder if it would be useful to make subselections: for example, for all waters placed newly with douse, show all waters that form no H-bonds.
  • H bond parameters:
    • font size for distances is a bit big (very crowded if there are several H-bonds)
    • "display as pseudo-bonds" on or off looked the same
    • The options for the representation of the bonds could be "hidden" (with a drop down?) or put below, as it may be less important than f.ex. the H bond parameters.
    • The "step" for angle is very small: 0.01 with the up/down button. Maybe use 1 degree?
    • Similarly, the step for bond lengths could be 0.1 A, not 0.01
  • Maybe the douse results menu can be a bit rearranged: the "douse only", "in common" etc choices could be placed at the top (as a row). This then leaves more space for the waters in the first column and the Hbond menu in the second column.
  • Add arbitrary douse/phenix arguments to executable launch
  • Work with new douse (the immediately preceding provides a means to use the new douse in the interim)
  • Provide a GUI/tool frontend to launch it
  • Allow generic use for examining waters w/o douse

Change History (11)

comment:1 by Eric Pettersen, 3 years ago

Priority is:

  1. Add arbitrary arguments, so that new douse can be tested/used
  2. Most pressing usability improvements, namely show next water after deleting one
  3. Refactoring for generic use, before too much gets baked in

comment:2 by Eric Pettersen, 3 years ago

Have made it possible to send arbitrary optional and positional arguments to the douse subprocess with the optionArg and positionArg arguments, which take string values and can be repeated in order to provide multiple strings. For instance, to send the optional argument "--citations iucr" (which is really two strings) you would add "opt --citations opt iucr" to the "phenix douse" command.

Last edited 3 years ago by Eric Pettersen (previous) (diff)

comment:3 by Eric Pettersen, 3 years ago

Made it go to the next water in the list after a [single] deletion (rather than all waters).

comment:4 by Eric Pettersen, 3 years ago

Finished refactoring to make separate tool possible. "Check Waters" tool will be in tomorrow's daily build.

comment:5 by Eric Pettersen, 3 years ago

Changed any sphere representations in the input/douse models to stick

comment:6 by Eric Pettersen, 3 years ago

Did the H-bond parameter requests, except for de-emphasis of pseudobond display options. This GUI is used by multiple tools, customized by GUI argument values, and making the requested change(s) would be a lot of work to avoid impacting other interfaces and didn't seem worth it.

comment:7 by Eric Pettersen, 3 years ago

As a side effect of Elaine's suggestions for improvements to the Check Waters tool:

  • Option to stay on current view after deleting waters
  • Button to unclip the view

comment:8 by Eric Pettersen, 3 years ago

Converter water list to a table that has an H-bonds column (again, from Elaine suggestion from Check Waters)

comment:9 by Eric Pettersen, 3 years ago

Also a density column now shown.

comment:10 by Eric Pettersen, 3 years ago

Put radio buttons across the top

comment:11 by Eric Pettersen, 3 years ago

Resolution: fixed
Status: assignedclosed

Launcher implemented

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