Opened 5 years ago

Last modified 4 years ago

#4306 assigned enhancement

Add graphical user interfaces for volumes, surfaces, higher-order structure

Reported by: Tom Goddard Owned by: Tom Goddard
Priority: moderate Milestone:
Component: UI Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Tom Goddard)

There are many Chimera graphical user interfaces that should probably be implemented in ChimeraX.
This ticket focuses on ones for volume data, surfaces and higher-order structure (Tools menu entries in those categories).

Here are the GUI interfaces not implemented in ChimeraX that are in those Chimera 1.15 menus.

Morph Map
Volume Filter - Gaussian, Median, Bin, Laplacian, Fourier, Scale, Flatten
Values at Atom Positions
Volume Series
Volume Tracer - partially implemented, missing Surfaces, Smooth, Transfer markers, Notes, ...

Surface Capping - subdivision, color, clip offset, disable

Icosahedron Surface
Small Angle X-ray profile - computed with Dina Schneidman FoXS web service
Flatten icosahedron - for making printed virus capsid models
Multiscale Models

Progress

These GUIs have been implemented

Scale Bar
Surface Color - radial/cylinder/height coloring, coloring by value or norm
Crystal Contacts - shows contacting subunits
Unit Cell
Measure Volume and Area
Volume Statistics

Change History (11)

comment:1 by Tom Goddard, 5 years ago

Description: modified (diff)

I added the Map Mean, SD, RMS menu entry and corresponding volume statistics command.

comment:2 by Tom Goddard, 5 years ago

Description: modified (diff)

comment:3 by Tom Goddard, 5 years ago

Added measure volume and area tool.

comment:4 by Tom Goddard, 5 years ago

Description: modified (diff)

comment:5 by Tom Goddard, 5 years ago

Description: modified (diff)

comment:6 by Tom Goddard, 5 years ago

Description: modified (diff)

comment:7 by Tom Goddard, 5 years ago

Description: modified (diff)

Added unit cell tool, and implemented unitcell command.

comment:8 by Tom Goddard, 5 years ago

Description: modified (diff)

Added crystal contacts command and gui.

comment:9 by Tom Goddard, 5 years ago

Description: modified (diff)

Added surface color gui.

comment:10 by Tom Goddard, 4 years ago

Added scalebar command and gui. #4883

comment:11 by Tom Goddard, 4 years ago

Description: modified (diff)
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