Chimera Requests and Ideas

This page lists ideas for new Chimera features and new documentation. Currently they include only those collected by Tom Goddard (focus on density maps, molecular assemblies, electron microscopy).

196. Convert molecule model to marker set
James Conway
July 16, 2009
Could sometimes use a command that converts a molecule read from a PDB file for example to a marker set.

195. Replicate markers using standard symmetry groups
James Conway
July 16, 2009
Have a command that can replicate markers placed with volume tracer using standard symmetry groups (icosahedral, cyclic, dihedral, ...).

194. Morph Map raytraced movie
Elaine Meng
July 13, 2009
Allow morph map record button to record a raytraced or supersampled movie. Currently there is no way to specify movie recording options.

193. Optimize fit-in-map memory use
James Conway
July 13, 2009
Only read partial volume data when fitting molecule or map into a much larger map that does not fit entirely in memory. Want fitting to automatically read volume data plus some padding that bounds molecule being fit. Have to update volume region if fit molecule moves outside of original box. Currently you can display a volume subregion and only it will be used in the fitting.

192. Mouse drag to change depth cue
Elaine Meng
July 10, 2009
Would like a mouse drag method to change the depth cue parameters continuously. Currently it involves typing new numbers in the Effects panel, or moving the clip planes which has the undesired consequence of turning on clipping.

191. Option to send single command
Chris Lau
June 25, 2009
Want to send a single command to an already running Chimera, for example, 'chimera --run "open 1zik"' or 'chimera --run "preset apply int 2"'.

190. Multiscale command.
Richard Marhoefer
June 17, 2009
Want to adjust transparency of multiscale surfaces and change display styles (e.g. to ribbon) using commands for movie making. Currently no commands can change multiscale surface color or display style.

189. Make Gaussian filter more memory efficient.
Mikyung Han
June 17, 2009
Make Gaussian filter more memory efficient. Currently it uses numpy fft library which only provides double precision, and can't transform in place. So 16 bytes per voxel are required. For single byte data that is 16x bigger than the input data. Could transform a plane at a time building 32-bit float array. This would also permit progress messages and canceling. Other improvements would be distributing 64-bit Mac Chimera or using fftw for fourier transforms.

188. Control grid spacing in resample command.
Jean-Paul Armache
June 10, 2009
Would like to be able to use a finer grid spacing in command "vop #0 resample onGrid #1". Maybe add a gridSpacing option.

187. Optimize transition transparency command.
Hernando Sosa
June 2, 2009
Changing molecule transparency with the "transition" command is very slow.

186. Save surface selection in sessions.
Elaine Meng
May 27, 2009
Making a surface with the shape command, selecting it, saving the session, then restoring the session produces an unselected surface.

185. Turn/move commands on subsets of atoms.
Tatyana Fedotova
April 30, 2009
Would like to rotate a helix about a fixed pivot. Make turn and move commands able to move only select atoms, not just whole models.

184. Warn if volume not shown at full resolution.
Ed Egelman
April 22, 2009
Show a warning if a volume data set is opened but not shown at full resolution. This warning could be shown just once (maybe a checkbutton option "don't show again") to familiarize new Chimera users with the volume step size parameter.

183. Command ` to focus next window on Mac. Implemented for Aqua April 24, 2009
Chuck Sindelar
April 20, 2009
Make "Command `" cycle the focus through the Chimera windows on Macs. This works in many other apps. "Shift Command `" (or Command ~) should cycle the reverse direction. The "Command `" works in Mac X11 Chimera in Mac OS 10.5.6, but "Shift Command `" does not. This is a (half-working) feature of Apple X11. Neither key works on Aqua Chimera.

182. Chimera command for playing MD trajectories.
Bala Subramanian
April 16, 2009
Would like a command for playing MD trajectories so that movie recording can be done while playing two trajectories in sync.

181. Faster transparent surface rendering.
Tom Goddard
April 15, 2009
Speed up transparent surface rendering by not resorting by depth each redraw. If the view direction has not changed more than a certain angle (maybe 30 degrees, experiment with value) use previous sort order.

180. Improve surface color memory efficiency.
Xiangan Liu
April 9, 2009
Allow per-vertex surface coloring to use 8-bit rgba component values instead of 32-bit float to save a factor of 4 in memory use. Bug report #7148.

179. 64-bit Mac Chimera version.
Xiangan Liu, James Conway, and about 20 others
April 9, 2009
Want 64-bit mac chimera version for handling large volume data. The 32-bit version generates frequent memory allocation errors when more than about 1 Gbyte of data is opened. Current Aqua Tk is based on the Mac Carbon toolkit which does not support 64-bit apps. This will require switching to Aqua Tk Cocoa which I've tested with Chimera in its current pre-alpha state -- all working except Togl. Bug report #7148.

178. Cubic interpolation of volume data.
Terry Lang
October 16, 2007
Allow volume values at atom positions tool to use cubic interpolation. Currently only supports linear interpolation. Bug report #4676.

177. Record movies across multiple Chimera sessions.
Elaine Meng
June 18, 2007
Allow recording frame images in several Chimera sessions and encoding a movie containing all the images. Bug report #4064.

176. Handle complex biological unit specifications.
Hongbo Zhu
December 7, 2004
Want Multiscale tool to handle PDB remark 350 BIOMT matrices where different chains have different transformation matrices (e.g. 1e79). Also want to handle cases of multiple biological units (e.g. 1gy7). More details in bug report #1344.

175. FFT better memory efficiency.
Benoit Zuber
April 13, 2009
An FFT of a 32-bit float map takes 8 times the memory of the original map because it produces a complex double precision results (4x) then the absolute value (2x), then cast to single-precision (1x), then recentering (1x). A variety of optimizations could reduce this although using a different FFT package like fftw would be needed to use single precision since our current numpy fft only supports double precision.

174. Handle complex volume data.
Benoit Zuber
April 9, 2009
Allow reading complex volume data (MRC format) for use in Fourier analysis.

173. Measure centroids and planes.
Bala Subramanian, David Chenoweth
April 8, 2009
Allow calculating centroid of selected atoms. Allow calculating plane fitting select atoms using least square fit, and calculating angles between planes. Could add these to the "measure" command and provide graphical depictions (sphere for centroid, rectangle for plane). Consider how this interacts with Eric's helix axis calculation.

172. Allow using markers without graphical user interface.
Daniel Russel
March 26, 2009
Make volume tracer Python calls available when Chimera started in no-gui mode. Currently volume tracer always tries to create its user interface dialog. Want this to use markers in non-interactive scripts.

171. Measure solvent accessible area from xray map.
Murali Ayaluru
March 26, 2009
Would like to compute the solvent accessible surface area from an x-ray map. Normally this is done from an atomic model. Possibly the same idea of rolling a probe sphere (modeling a water) over an xray map contour surface. An alternative definition might consider the density within the probe sphere.

170. Measure contact areas between surfaces.
Tom Ferrin
March 26, 2009
Want a command to determine the connected pieces in a scene containing multiple surface models. Intersecting surfaces are considered connecting and the contact areas should be reported. This would be used for determining when 3-d printed models would fall apart or have weak joints.

169. Export multi-color surfaces in Wavefront OBJ format.
Damien Lariviere
March 23, 2009
Have export of wavefront obj format write out per-vertex color information. Currently only a single color is written for each surface piece.

168. Blend multi-wavelength volume data.
Benoit Zuber
March 16, 2009
Want to be able to blend matching planes from 2 or more volume data sets (confocal images). Also want plane slider to control which plane is shown for multiple data sets.

167. Mouse mode to center on atom.
Sirano Dhe-Paganon
March 16, 2009
Want a mouse mode where clicking on an atom causes centering on that atom without zooming.

166. Set contour level for specified enclosed volume.
Andrej Sali, others
Feb 25, 2009
Command to set volume contour level to achieve a specified enclosed volume.

165. Mouse mode to delete connected markers.
Juha Huiskonen
Feb 25, 2009
Would like a mouse mode to click on a single Chimera marker (created with volume tracer) that deletes that marker and all other markers connected by links.

164. Make fitting move additional models.
Keren Lasker
Feb 17, 2009
When fitting one atomic model into a map, want to drag along other atomic models maintaining their same relative orientation to the model being fit.

163. Zone outside radius.
Jean-Paul Armache
Feb 10, 2009
Would it be possible to do an inverse zone? I mean it in the sense that instead of zoning and displaying only the density within a specified distance from the structure, display everything else.

162. Difference map when fitting.
Paul Dreizen
Jan 6, 2009
The "Fit model to map" module in the last 2 versions allows density maps to be constructed from atomic models. Would it be feasible to calculate a "difference map" between the brix density map from cryoEM data and the Chimera-constructed density map from atomic models? This difference map might show large peaks and valleys in an overview, which might very much help to distinguish the best among several density fits that are structurally different but near-equivalent numerically.

161. Add two volumes.
Martin Kampmann
Dec 9, 2008
Improve vop command to allow adding two volumes with differing grids. For example, "vop #0 add #1 extend true sample true multiplier 0.25".

160. Surface cappping command.
Gabe Lander
Sept 9, 2008
Make command to turn on/off surface capping. Also to set color, style, subdivision of caps.

159. Handle volume series as a single data set.
Sebastian Haase
July 21, 2008
Would like volume series handled as a single data set instead of separate data sets for each time point. Want a single histogram shown in volume dialog which changes based on the current time being shown.

158. Add origin parameter to shape command. Implemented October 17, 2008
Ed Brignole, Elaine Meng
July 17, 2008
Origin keyword argument in shape command could take 3 comma-separated numbers or an atom spec. For numbers, might have a coords keyword to specify a model id for local coordinates.

157. Turn command center of rotation argument. Implemented October 17, 2008
Haixin Sui
July 15, 2008
Allow turn command to specify center of rotation in local coordinates for a specified model. Also have argument to move only specified models. Used for rotation microtubule volume about symmetry axis. Also would need rotation axis to be in local coordinates. Could have a few new keyword arguments similar to the mclip command. Also allow "cofr" command to specify explicit coordinates in local or global coordinates.

156. Volume rotation in Euler angles.
Haixin Sui
July 15, 2008
Allow volume rotation of local coordinates to be specified in Euler angles. Currently must be specified axis vector and rotation angle.

155. Volume origin in index units. Implemented September 9, 2008
Haixin Sui
July 15, 2008
Allow volume data origin xyz = 0,0,0 to be specified in grid index units. This is convenient for EM data where symmetry axis location is known.

154. Create PDB copies covering map.
Christian
July 15, 2008
Use crystal symmetry to create copies of PDB model to cover all density in an x-ray map.

153. Crystal map sigma units.
Terry Lang, several others
July 15, 2008
Allow volume values to be scaled so 1 equals 1 sigma (root mean square of all map values). Want this in volume viewer and surface color and volume command and every place that volume values are used. So the scaling should probably be part of the grid data object.

152. Periodic covering map command.
Terry Lang
July 15, 2008
Make a command that creates a map covering a PDB model using a periodic map (unit cell x-ray map). There is already a keyboard shortcut "bv" to do this but a command would be a more familiar user interface and allow specifying the padding value (bv makes padding 5 Angstroms).

151. Tile newly opened models.
Eduardo Sanz Garcia
July 3, 2008
Want option to tile newly open models by default. Also want tile border scale saved between sessions. Used for viewing progress of single particle reconstructions.

150. Space Navigator on Linux.
D Greening
July 14, 2008
Want space navigator support on Linux.

149. Place markers on surfaces.
Daniel Hautzinger
July 11, 2008
Place markers on a surface. Wanted for AFM data. This case actually probably better handled by existing capability to place on data planes. But other applications could use placement on surfaces such as highlighting features on membranes seen in tomograms.

148. Pipes and planks coloring.
Gary Ren
June 26, 2008
Allow selection and coloring of individual helices, strands, turns in pipes and planks model. Could be implemented by using a SurfaceModel instead of VRMLModel. Requested for showing low resolution model in EM map.

147. Calculate difference map. Implemented June 18, 2008
Jean-Paul Armache
June 2, 2008
Want to subtract two maps that have identical grids. Could be added to "vop" command.

146. Add torus to shape command.
Pradeep Pallan
May 12, 2008
Want to show a circle to indicate size of a molecular structure.

145. Don't include hidden surface in area/volume.
Ed Brignole
May 12, 2008
Make the measure area/volume dialog include only the displayed surface. So if the hidedust.py script hides some surface components, they will not be included in the reported values.

144. Report area/volume in volume dialog.
Ed Brignole
May 12, 2008
I have a request for display of the measure volume area tool - can it be moved from "tools" to "features" such that it is displayed in the volume viewer along with color, voxel size, etc. The problem I have is that frequently I have 30 or so volumes to open at once and then need to independently go through them and set density thresholds. It's really a pain to have to select the volume once in the volume viewer and then again select the same volume in the measure tool then go back to the viewer and adjust threshold. After doing this 30 times, you'll find that most of the effort is spent making sure to select the same volume in both menus so that the selected volume that you are adjusting is the same volume being measured.

143. Command for running keyboard shortcuts. Implemented April 8, 2008
Jean-Didier Marechal.
March 27, 2008
Would like a command for running a keyboard shortcut. Makes shortcut capabilities easily accessible from a script. Could extend "ac" command.

142. Enable shortcuts for volume eraser.
Weimin Wu.
March 26, 2008
The volume eraser dialog says to use shortcut "es" to erase but shortcuts are not enabled by default and it is not clear how to enable them. Might put an "enable shortcuts" button on dialog or enable them automatically when dialog is shown.

141. Optimize volume grid spacing to best fit a molecule.
Stefan Backstrom.
March 26, 2008
Would it be possible to optimize the a/pix, or scale value when one is fitting either a map in map, or model in map ? Often it seems as if the scale is not 100 % correct between a crystal structure and a cryo-EM reconstructinon, and it would be nice to be able to choose to fit the scale of the EM-map at the same time as the fit rotation and translation.

140. Fit molecules in map avoiding steric clashes.
Andrea Rossi.
March 13, 2008
In low density map, place one molecule and locally optimize the fit another without causing clashes with those already placed.

139. Volume eraser undo.
Htet Khant.
March 11, 2008
Undo button on volume eraser dialog to avoid having to save map frequently.

138. Add per-model clip command "frames" argument.
Eric Pettersen.
February 22, 2008
The mclip command could use a "frames" argument, for moving the plane smoothly during an animation. Tom G notes: A frames argument for mclip would be neat. Hard to do it right I think. If you just turned on clipping for the first time with frames 10, you might reasonably expect to see the model progressively clipped along the specified axis. Likewise if you enabled slab with frames = 10 something neato and applesque might happen. Of course I could go the easy road and make the on/off transitions happen in the first frame. And then there is the vanilla change of axis (clip plane rotates), change of origin (plane translates), change of slab thickness -- easy part I think. Elaine notes: You could accomplish such a transition with savepos/reset now that "positions" include per-model clipping planes. However, it requires more planning ahead and saving a session for later reproducibility...

137. Two per-model clip planes for wedges.
Tom Goddard.
February 14, 2008
Would be useful to have two or more (as supported by hardware) per-model clip planes for showing wedges of volumes. Needed for nuclear pore with wedge cut out.

136. Less sensitive solid volume brightness / transparency. Implemented February 15, 2008
Jeff Triffo.
February 14, 2008
Solid rendering transparency greatly changes appearance with histogram node height change of 0.99 to 1.00. Need new definition of transparency factor to make this less sensitive.

135. Angle dependent transparency.
Andrew Jewett.
February 14, 2008
Scale surface opacity for oblique viewing angles. (1-alpha) <- (1-alpha)**(1/|cos(theta)|). Tried this with opacity.py script for current viewing angle. Very nice darkening of edges. Could be implemented as an opengl shader.

134. Output volume solid brightness curve.
Jeff Triffo.
February 14, 2008
Output volume transfer function (yellow curve on volume dialog histogram) numeric values for node heights so they can be reused on other volume data sets using the volume command. Basic need is to apply transfer function from one map to another.

133. Color by atom on surface caps.
Elaine Meng.
February 14, 2008
Colors surface caps of molecular surfaces by nearby atom colors.

132. Make capping on by default for per-model clip planes. Implemented November 4, 2008
Tom Goddard.
February 8, 2008
Would like to have capping of clipped surfaces on by default. Trouble is that rotations of models can be slow since intersection with near clip plane has to be constantly recomputed even when no clipping is happening. This should not be a problem with per-model clip planes, so capping could be enabled by default in that case. Would want the capping option to appear in the per-model clipping dialog. Perhaps have a capping options button too to control subdivision, cap color, ....

131. Different colors for surface inside and outside.
Ian Yarbrough.
February 4, 2008
Allow surfaces to have different colors on their two sides. Main difficulty is in providing a user interface. OpenGL supports coloring the sides of surfaces differently.

130. Make crytal map and PDB model coincide. Implemented Nov 20, 2007. Keyboard shortcut "bv" creates covering map.
Trevor Sewell, Terry Lang.
February 4, 2008
Programs O and Coot will move a crystallographic unit cell map to cover a displayed PDB model (or selected atoms). Coot can also wrap the map if the model straddled the unit cell map boundary. These behaviors are automatic in those crystallography programs. Should allow Chimera to do this in an easy way. Another option is to move the PDB by unit cell translations into the map. Worth supporting both methods.

129. Read brix maps as 8-bit values.
Thomas Becker.
February 4, 2008
Have an option to load brix maps as 8-bit values without applying the shift and scale factors in the header that produce 32-bit float values. This would save a factor of 4 in memory use and is how Chimera behaved prior to version 1.2470.

128. Surface transparency with color zone.
James Fethiere.
January 30, 2008
Its currently cumbersome to make a color zone colored surface transparent. Atoms or markers must be given a transparent color. Some overall transparency control (as done with molecular surfaces with the Actions / Surface / Transparency menu entry) would be useful. The Action menu entry for surface transparency has no effect when the Surface Color dialog is coloring the surface (e.g. by electrostatics). This is confusing.

127. Label unit cell axes and show cell offset.
Dirk Kostrewa.
January 30, 2008
Have the outline box created by the unit cell dialog indicate the a,b,c axes and origin. Maybe color those 3 edges from the origin red, green and blue. Also indicate how much the shown outline is shifted, e.g. origin (A,0,0) or (A,2B,-C) or (0,0,0).

126. Place markers on any visible volume.
C Akey.
January 25, 2008
Make volume path tracer place markers on any visible volume instead of just the one highlighted in the volume dialog. The current behaviour is especially annoying when the highlighted volume is undisplayed.

125. RGB TIFF image file reader.
Sebastian Haase.
January 23, 2008
Read RGB tiff image files as 3 scalar volume data sets.

124. Extend map using symmetry.
Francesco Zonta.
January 18, 2008
Would like to be able to replicate a map containing a crystallographic asymmetric unit using space group symmetries and unit cell translations to cover a larger region. The program Coot does this. In Chimera could add a command that builds a new map covering a specified block of unit cells from the asymmetric unit map. Would be nice to support this for EM single particle reconstructions also, for example, building full icosahedral map from a partial map and symmetry operators.

123. Color using MolMol electrostatic potential.
Esther Bullitt.
January 16, 2008
Read MolMol electrostatic potential grid data for coloring molecular surfaces. Format is very simple and is described in MolMol ReadPot manual page.

122. Multi-page TIFF image file reader. Implemented January 22, 2008

Sebastian Haase.
January 15, 2008
Read multipage tiff image files as volume data. Sebastian provided example Python code for reading such files.

121. Correlation for fitting model in map. Implemented February 21, 2008
C Akey.
January 14, 2008
Use cross-correlation coefficient to fit atomic model in map. Will require making simulated map at target map resolution.

120. Area/volume command.
Zhiya Sheng.
December 26, 2007
Make a command for reporting surface area and enclosed volume.

119. Crystal lattice command.
Jack Johnson.
December 20, 2007
Make a command to create copies of atomic models to fill a crystal lattice.

118. Icoshedron mesh command. Implemented January 24, 2008 (shape command).
Jack Johnson.
December 20, 2007
Make a command equivalent to the icosahedron surface tool.

117. Hide all models button.
Eduardo Sanz Garcia.
November 26, 2007
Make clicking on "Shown" heading in Model Panel hide all models. Possibly hide all if all are shown, show all if some or all are hidden.

116. Easy hiding of all but one volume.
Eduardo Sanz Garcia.
November 26, 2007
Might make right click on show/hide oval above histogram hide all other volumes and show this one (when initially in hidden state). This makes it easy to look at just one volume.

115. Scrollbar for volume histogram panels.
Eduardo Sanz Garcia.
November 26, 2007
Would like a vertical scrollbar to control which volume histograms are shown when there are more than the maximum number of histograms (default 3). Scrollbar could offer just discrete positions so you would never see half of a histogram. For high speed with many volumes open the out of view histograms would not be created until visible. Implementation would probably just reuse the existing 3 canvas widgets. Volume names could update immediately while histogram redisplay is displayed to allow very fast scrolling. Scrollbar should only appear when additional volumes are present. With scrollbar, might keep order of volume data sets fixed, instead of the current somewhat confusing scheme where the least recently active volume histogram disappears when a new volume is chosen from the Data menu.

114. Save color palettes.
Jeff Triffo.
November 26, 2007
Want to save color editor colors that are place at the bottom of the dialog. These are normally saved in the Chimera preferences file. Would like to save them and load them from a different file.

113. Animation extracting octant from virus density.
Yen-Chywan Liaw.
November 15, 2007
Wants to be able to extract an octant from a virus map. Both pieces remain visible as the octant moves radially out and is rotated to see layered structure.

112. Animation where ligand flies into bound state.
Yen-Chywan Liaw.
November 15, 2007
Have receptor crystal structures with and witout ligand. Want to be able to make a movie that starts with unbound receptor and distant ligand and has ligand move into receptor which simultaneously morphs to bound receptor conformation.

111. Want easy way to morph both volume and pdb model.
Haixin Sui, Yen-Chywan Liaw.
November 15, 2007
The morph map and morph conformations tools can morph density maps and atomic models. But it is challenging to play both morphs in sync for making an animation. Want it to be simple to morph both, where the atomic models have been fit into starting and ending volume data sets.

110. Reverse order of colors in surface color tool. Implemented April 17, 2008.
Yen-Chywan Liaw.
November 15, 2007
Would like a button to reverse the order of colors in the surface color tool, for instance, to get blue->red instead of red->blue.

109. Make POVray appearance better match Chimera window.
Ed Egelman, others.
November 15, 2007
Raytraced transparent volume surface images with povray have very different transparency and brightness than what is seen in the Chimera window. Since raytracing with transparency is extremely slow, it is difficult to test many combinations to get the desired appearance.

108. Set contour levels for multiple volumes at once.
Steve Ludtke.
November 15, 2007
Want to set the same contour level for several volumes (single particle reconstructions). Told Steve about new volume command tha can do this. Would be nice to have a way to do this in graphical user interface.

107. Set morph map contour level to preserve enclosed volume.
Pawel Penzcek.
November 15, 2007
Add option to preserve enclosed volume when using morph map. Volume series tool already has this so some code is already available.

106. Read PRIISM format volume files with WZT disk layout. Implemented June 3, 2008.
Sebastian Haase.
November 15, 2007
The current Chimera priism file reader only handles ZWT order (Z = z planes, W = wavelengths, T = times) and refuses to read other orders. Sebastian wants it to read WZT order. This is for multiwavelength light microscopy.

105. Command to print relative model orientation.
Duncan Sousa.
November 13, 2007
Add command to print relative model orientation: rotation angle, axis, shift. Might support alternate formats like rotation matrix / shift.

104. Cubic volume interpolation.
Terry Lang.
October 23, 2007
Add cubic volume interpolation at points as alternative to trilinear interpolation. Want this for searching for alternate side-chain conformations in x-ray maps.

103. Fit using correlation.
Alexander Solodukhin.
October 1, 2007
Fit map in map using correlation instead of overlap so that fit is not simply pushed to high density region with poorly matching shape.

102. Thick surfaces.
Jeff Triffo.
September 19, 2007
Allow making surface have finite thickness for showing membranes. Would probably start with IMOD surface. Would be relatively easy to duplicate surface moved along surface normals, and create an edge band connecting the two surfaces. More work to be able to delete thick surface, save it, or change its thickness.

101. IMOD session saving.
Jeff Triffo.
August 20, 2007
Want IMOD surfaces that have been recolored in Chimera saved in session files.

100. IMAGIC-5 volume file reader.
Michael Schatz.
July 13, 2007
Write volume file reader for the em2em native IMAGIC-5 file format.

99. Nintendo Wii controller for volume fly-through. Tested with DarwiinRemote September 27, 2007
Dan Greenblatt.
July 10, 2007
Interface the Nintendo Wii controller (6 degree of freedom, accelerometers and infrared pointing direction using base station emitter), wireless, bluetooth, $40, as a Chimera input device.

98. Contour surface, include box boundaries. Implemented October 9, 2007
Tom Goddard.
July 3, 2007
Cover holes left when contour surface extends to boundary of volume. Have contour calculation add surfaces coincident with faces of volume box where needed. This will give the contour surface a solid appearance and allow capping slices without encountering open boundary loops.

97. Volume fly-through controls.
Manfred Auer.
July 2, 2007
Allow fly through navigation controls for EM tomography data. Could use game controller input device.

96. Better error message when volume data too large. Done August 23, 2007
Irina Serysheva, Matt Dougherty.
June 28, 2007
Provide a simple error message instead of a Python traceback when the memory allocation fails in reading a large volume array.

95. Color IMOD surfaces with Actions/Color menu.
Jeff Triffo.
June 28, 2007
Would like to be able to color selected IMOD surfaces with the Actions / Color menu. Can use "co" keyboard shortcut currently.

94. Help buttons on volume viewer panels.
Elaine Meng.
June 4, 2007
Want "?" buttons next to the "x" buttons on volume viewer panels that show the appropriate subsection of the volume viewer user's guide page.

93. Simplify volume data Python calls. Many improvements August 23, 2007
Gabor Papai.
May 24, 2007
Want simpler python calls to open maps and perform common actions. I wrote a script for Gabor to fit a map in another map (fitnogui.py) that is 70 lines, seems longer than should be necessary.

92. Make multiscale tool work when atoms deleted. Implemented October 25, 2008.
Andy LiWang.
May 24, 2007
Make multiscale tool not raise errors when atoms are deleted with Actions/Atoms+Bonds/delete after multiscale model created. Chimera but report 3915 and 3490.

91. Save image without Chimera window shown.
Jawahar Swaminathan (MSD).
May 24, 2007
Want to save Chimera images in nogui mode (no Chimera window shown) to make virus capsid images for Macromolecular Structure Database.

90. Display 2-d contour lines on clipped volume surfaces. Implemented September 9, 2008
Yao Cong.
May 22, 2007
Display 2-d contours on clipped volume contour surfaces. A prototype could probably be implemented in less than a day. Interpolate the map on the clip plane on a rectangular grid. Rectangle determined by bounds of plane intersection points with volume box edges. Sample at perhaps half of minimum volume grid spacing. Make a 3-d map with 2 planes with same interpolated data, contour with 3-d contouring code, and display as surface band as mesh with only one band edge shown. Combine multiple 2-d contour levels in a new surface model.

Simpler approach implemented. When displaying a single xy, xz or yz volume plane (e.g. using the volume planes panel) with mesh style and options "cap high values at box faces" off and "mesh lighting" off, get 2-d contour lines for that data plane. Can add more contour levels using ctrl-click on volume dialog histogram. Can show plane together with 3-d data by duplicating the volume data set (volume dialog File / Duplicate) and using the region bounds panel to limit the part of the 3-d data displayed.

89. Make experimental plugins check Chimera version compatibility.
Eric Pettersen.
May 22, 2007
We've received 5-10 bug reports from people using plugins from the experimental features web page with versions of Chimera older than that requires as listed on the download page. Would help if each plugin did a check when it is invoked to see that a sufficiently recent Chimera is being used, and warn if version is older than required.

88. Show map standard deviation. Menu entry to print mean/SD values October 10, 2007
Holland Cheng.
May 5, 2007
Indicate map mean and standard deviation using tick marks on volume dialog histogram. Also have option to show map values in standard deviations from mean. Mean and standard deviation would be computed for entire volume even though extra padding around the structure will effect computed values.

87. Raw map file reader.
Request at UC Davis bay area cryoEM meeting.
May 5, 2007
Allow reading "raw" maps -- file containing 3-d array of numbers. User will specify grid size and data value type (float32, int16, uint8) when file is read.

86. Amira segmentation file reader.
Request at UC Davis bay area cryoEM meeting.
May 5, 2007
Add file reader for Amira segementation files.

85. Fetch PDB biounit files.
Tom Goddard
April 23, 2007
Add fetch by id for PDB biounit files.

84. Thicker silhouette edges. Done July 28, 2007
Tom Goddard
April 20, 2007
Provide user interface to control thickness of silhouette edges. Often want thicker edges. Can achieve this now by a trick -- making the screen image very small and specifying a much larger size in the Save Image dialog. The clathrin image gallery entry illustrates a case where the thicker edges are desirable.

83. Warn about ambiguous transforms.
Preethi Chandramouli, Tom Goddard
April 19, 2007
When a new model is opened in Chimera and is given an initial transform equal to that of the model with the lowest id number, and other models have differing transforms, warn about this in a status line message. For example: "1grl.pdb transformed as groel.mrc". Many users are confused when misalignments occur because of this "match the lowest id number" rule. That rule is not intuitive.

82. 2-d overlays and labels on molecular surfaces.
Tom Goddard
April 18, 2007
Add ability to draw residue outlines and residue text labels on molecular surfaces as illustrated in

• Xiao C, Rossmann MG.
  Interpretation of electron density with stereographic roadmap projections.
  J Struct Biol. 2006 Oct 24; [Epub ahead of print]

which projects such annotations for virus capsids onto a sphere. Also would like to overlay coloring by electorstatics, contour lines from density maps, symmetry axis annotations. These 2-d overlays on surfaces convey alot of information. Could have an option for no lighting to give 2-d appearance for easier image comprehension. Flat shaded renderings with chain level edge highlighting for depictions with the multiscale tool would be interesting.

81. Calculate density map for molecule. Implemented January 14, 2008.
Thomas Marlovits
April 17, 2007
Add tool to calculate a density map from a molecule (PDB) model. This already exists in the AIRS / EMAN Chimera extensions (called PDB to MRC) but it requires installing EMAN. Would like the capability available in standard Chimera distribution. Would be useful for fitting molecules into maps using the fit-map-in-map tool.

80. Trace protein backbone.
Matthew Baker
April 12, 2007
Want to position markers corresponding to CA atoms within 4-8 A density maps. Matt does this with crystallography program COOT right now and it is very tedious. Needed features: display distances to previous and next CA, display distances to nearby CA within 4A, move CA to density maximum, move range of markers for alpha helix to best fit in density. Distances update in real time, moves can be undone. Matt would refine python code given an initial prototype.

79. Multiple graphics windows.
Xiaoyun Chen
April 12, 2007
Want separate graphics windows for three orthogonal views: xy, yz and xz.

78. Path tracer markers.
Eric Pettersen
April 12, 2007
Put each path tracer marker in a separate residue to allow commands that use residue numbers to handle consecutive series of markers.

77. Path tracer marker attributes.
Jeff Triffo
April 12, 2007
Want to be able to define attributes of volume path tracer markers, such as, "is_filament=True", "filament_number=1", "branch_point=False", ... for structures traced in electron tomography data. These should be saved in session files and marker XML files. Want to make selections based on attribute values. Should interoperate with the existing atom attribute commands setattr, defattr, calcattr, the Render/Select by Attribute tool, attribute atom specifications (e.g. "@/bfactor>=50"). Marker xml file read/write currently preserves unknown marker, link and marker set tags.

76. Fetch EMDB maps.
Cathy Lawson
April 12, 2007
Add fetch by id for EMDB maps. Would want fetch in background with progress dialog and cancel button and save to a user-specified fetch directory to avoid repeated fetching of large maps.

75. Fetch PQS biological assemblies. Implemented April 27, 2007
Miguel Ortiz Lombardia
April 12, 2007
Add PQS biological assembly files (*.mmol) to fetch by id.

74. Volume rendering size limit.
Tom Goddard
April 12, 2007
Solid rendering 2-d em micrograph of size 2916x4374 showed white rectangle at full resolution on Intel Mac laptop, mac os 10.4.9 I think due to OpenGL texture size limit. Warn user about this.

73. Color surface pieces.
Anindito Sen
April 12, 2007
Make pick surface pieces surface coloring save in session files.

72. Biological assemblies in mmcif.
Cathy Lawson
April 12, 2007
Make multiscale use assembly info from mmcif file for viruses. mmCIF version 3 files for virus structures have pdbx_struct_assembly records such as 'complete icosahedral assembly', 'icosahedral asymmetric unit', icosahedral pentamer', 'icosahedral 23 hexamer', 'icosahedral asymmetric unit, std point frame', 'crystal asymmetric unit, crystal frame'. A new notation for the symmetry was introduce in summer 2008 that may be more machine readable.

71. Reoriented density maps. Done for MRC and HDF formats September 4, 2007
Tom Goddard
April 12, 2007
Include rotation in written map header when resampled piece of volume extracted with addmaps command.

70. Subsample volume data, netcdf. Done with HDF, netcdf deprecated September 11, 2007
Matt Baker
April 12, 2007
Make netcdf writer automatically save subsampled versions of map in file down to size about 1 Mvoxels. Will want to save plane by plane so that file larger than what will fit in memory can be opened and saved.

69. HDF map file reader. Done August 7, 2007
Matt Dougherty, Pawel Penczek
April 12, 2007
Put HDF file reader in Chimera. Support netcdf type header fields for voxel size and origin, .... Support subsampled matrices in same file. Try this with PyTables Python wrapper of HDF. Add support for reading SPARX format hdf volume data. Tried this 3/21/2007 and found EMAN 3-d array layout backwards. Steve Ludtke is fixing.

68. Radial density plot. Made radial density calculation script March 2, 2007
Padma Natarajan
April 12, 2007
Incorporate radial average density plot for virus em maps into viper image creation script for making radial plots for VIPER web site. Could export text file (radius, ave density) to gnuplot. Would like to be able to display radial density plots in Chimera. Tried matplotlib which makes nice plots (with SVG, PNG, PS ... export). Mac installation ~80 Mbytes.

67. Setting figure magnification.
Christopher Akey
April 12, 2007
Add resetscale command that only restores camera scale to value saved in session file (or 1.0 with no session value). Used for achieving standard magnification in multiple related figures.

66. Save BRIX format. Added prototype BRIX writer October 19, 2007
Christopher Akey
April 12, 2007
Write maps in BRIX format. This is for interoperation with O for building models in EM maps.

65. User-defined surfaces. Implemented January 30, 2008.
Jeff Triffo
April 12, 2007
Create surface from volume path tracer markers. Used for electron tomography annotation.

64. Save more EM map file formats. Christos Gatsogiannis
April 12, 2007
Write additional volume file formats (situs, imagic).

63. Arrows on morphed maps.
Tom Goddard
April 12, 2007
Make 3-d arrows at morph map surface points of maximum change. Implementation: Look at difference of end-point maps interpolated on surface and smoothed over surface, find extrema, and place BILD arrows, maybe in separate models for easy undisplay of individual arrows.

62. Volume viewer code clean-up. Done August 9, 2007
Tom Goddard
April 12, 2007
Simplify volume viewer code by using Checkbutton_Entries from Hybrid.py.

61. Benchmark scores. Implemented May 2, 2008.
Tom Goddard
April 12, 2007
Change benchmark code to display models and include the Chimera event loop -- ie use actual timings. Current surface scores are vastly inflated due to graphics driver optimizations that shortcut rendering when no screen display occurs.

60. Color zone slider range. Implemented October 3, 2007.
Jeff Triffo
April 12, 2007
Make color zone set the maximum slider value based on the diameter of the displayed surface.

59. Copying volume display settings.
Jeff Triffo
April 12, 2007
Provide way to copy volume settings (thresholds, colors, styles, brightness, transparency, rendering options) from one volume to another, for example, from a volume to an externally filtered version of that volume.

58. Map plane display.
Jeff Triffo
April 12, 2007
Allow averaging together neighboring planes in em tomography when displaying a single slice to improve signal to noise.

57. Slicing EM maps. Resample volume added September 4, 2007
Jeff Triffo
April 12, 2007
Allow plane slicing of em tomography at arbitrary angles. Karin Gross and Christoph Best at Max Planck Institute for Biochemistry have written a Chimera extension to do this. Web site.

56. Volume zones, solid rendering.
Jeff Triffo
April 12, 2007
Make volume zones work in solid display mode.

55. Save marker sets relative to models.
Heather McCune
April 12, 2007
Allow writing marker set XML positions relative to volume data coordinates. Change save marker set dialog to offer "relative to" choice like Save PDB dialog. Also allow choosing which marker sets to write. Simplest approach might be to copy ModelPanel/writePDBdialog.py and modify it.

54. Volume rendering memory use. Implemented September 6, 2008.
Tom Goddard
April 12, 2007
Make solid rendering using 8 bit int rgba instead of float to handle larger volume sizes and increase speed. Default mode is currently to use 256 color colormap. So memory savings may be only for non-default settings.

53. Clip plane motion user interface.
Jeff Triffo
April 12, 2007
Make buttons and sliders to control perpendicular axis and translation of per-model clip planes for volume data.

52. Update graphics driver bugs web page.
Tom Goddard
April 12, 2007
Search closed chimera bugs for graphics driver issues and add them to the graphics driver bug page.

51. Crystal contacting chains. Partially done October 10, 2007 (crystal contacts tool).
Miguel Ortiz-Lombardia
April 12, 2007
Create all crystal chains within a given radius of an asymmetric unit. Allow loading just contacting chains rather than full asym units. Allow moving contacting units radially to show contacts.

50. Atomic force microscope file reader.
Alberto Roca
April 12, 2007
Put nanoscope AFM tools on experimental features page. Will need documentation.

49. Unit cell outline box.
Meshmol command can serve October 10, 2007
Sabuj Pattanayek
April 12, 2007
Add unit cell outline box color and line thickness controls to Unit Cell dialog.

48. Contouring optimization. New optimized algorithm October 2, 2007
Tom Goddard
April 12, 2007
Check if _contour speed changes much with -O3 compilation versus the current default of -O. Benchmark contour calculation at various ratios of triangle count to voxel count. I've only optimized for the low ratio scenario. May be that the high ratio case can be sped up significantly. Could use radial decaying sine curve and a range of thresholds.

47. Volume subsample voxel origin.
Tom Goddard
April 12, 2007
Fix precomputed volume subsample handling so that the subsample can be either at the corner or middle of the cell. The middle is appropriate if the subsamples represent average/max/median cell values, while the corner is correct if the sample is the value at the corner. Should allow arbitrary offsets to support saving subregions with subsamples.

46. Multiple volume dialogs. Multiple volume histograms added August 10, 2007
Basal Devkota
April 12, 2007
Allow two or more volume viewer dialogs for adjusting multiple maps easily.

45. XYZ axis display.
Jeff Triffo, Haixin Sui
April 12, 2007
Add a tool to make axes arrows using BILD, ala VMD to indicate orientation.

44. Better multiscale surface quality.
Tom Goddard
April 12, 2007
Allow multiscale surfaces to be higher quality by binning at a finer scale and distributing each atom over several nearby bins maybe with gaussian fall-off. This could use molmap command.

43. Reading large maps. Done July 31, 2007
Irina Serysheva
April 12, 2007
Make volume subsampling not allocate unsubsampled array when reading from file. Limits reading of large data sets.

42. Collaboration descriptions.
Tom Goddard
April 12, 2007
Add VIPERdb and EMDB collaboration web pages to CGL Research index.

41. Measure enclosed volume. Added keyboard shortcuts mv and ma September 29, 2006
Tom Goddard
April 12, 2007
Add option to measure volume/area to only measure selected surfaces.

40. Icosahedron surface session saving. Added December 5, 2008
Tom Goddard
April 12, 2007
Add session saving to icosahedron tool.

39. IMOD file reader. Added to distribution October 5, 2007
Masako Terada
April 12, 2007
Put IMOD segmentation surface file reader in Chimera distribution.

38. Image sequence file reader. Added TIFF stack reader July 21, 2007
William Beaver
April 12, 2007
Add image sequence (tiff, pnm) volume file reader.

37. Color zone with multiple radii.
Hernando Sosa
April 12, 2007
Consider allowing sequences of colorings in color zone. Would allow using multiple radii. Also greater flexibility in coloring.

36. Make chains become separate molecules. Added to distribution October 10, 2007
Elaine Meng
April 12, 2007
Add split molecule command to Chimera distribution. Makes each chain a separate molecule. Currently on experimental features web page. split.

35. Delphi Controller surface coloring. Implemented April 25, 2007.
Elaine Meng
April 12, 2007
Make DelphiController show potential on MSMS surface with Surface Color tool. Currently potential is shown with volume viewer.

34. Print map values.
Nihshanka Debroy
April 12, 2007
Allow clicking on a surface to print volume value at the corresponding surface point, for example electrostatic potential.

33. Surface coloring key. Implemented July 15, 2008.
Alexander Rusnak
April 12, 2007
Add color key to surface color tool using surface strip.

32. Movie recorder format compatibility. Powerpoint movie fixes documented March 2, 2007
Tom Goddard
April 12, 2007
Investigate usability of Movie Recorder output formats on all common platforms Windows, Mac, Linux. See which work on stock operating system installations, which require codec downloads, which movie players will work, and which won't work without extreme effort.

31. Switching volume dialog volume.
Jean-Francois Menetret
April 12, 2007
Have volume viewer automatically switch to show most recently displayed volume (switched perhaps in Model Panel) in volume dialog.

30. Volume commands for movies.
Frank Albers, Jeff Triffo
April 12, 2007
Want volume commands for making animations. Wants color fades. Want per-model clip plane transitions.

29. Volume bit masks.
Tom Goddard
April 12, 2007
Have bit mask with 32 bits per density map voxel, each bit representing different masks. Could for example make masks from feature analysis tool that finds cylinders, spheres, planes, ....

28. Mask volume with cylinder. Implemented October 17, 2007 (mask and shape commands).
Haixin Sui
April 12, 2007
Masking density to cylinders, masking with an external mask file. Used for cylindrical virus particles.

27. Fit selected atoms in map.
Several users
April 12, 2007
Add option to fit model in map tool to move only selected atoms.

26. Buried surface area.
Tom Goddard
April 12, 2007
Tool to report buried surface areas between two chains, between 1 chain and all contacting chains, or between all pairs of contacting chains.

25. Multiscale chain coloring.
Tom Goddard
April 12, 2007
Add color by sequence and extend selection to same sequence to multiscale. Might provide a sequence of colorwells for colors to use in color-by-chain-id and color-by-sequence. Currently have xc keyboard shortcut to extend multiscale selection to chains with identical sequences.

24. Electrostatic potential coloring. Similar fix made May 6, 2008.
Elaine Meng
April 12, 2007
Make Electrostatic Surface Coloring menu entry prompt for potential file as soon as it is started. Otherwise user thinks they can just press Color and Chimera will compute the electrostatics.

23. MSMS surface calculation with stand-alone program. Implemented March 18, 2008.
Tom Goddard
April 12, 2007
Check if msms standalone program crashes in any cases where library crashes. Look at program source code to see if library can be configured to use same settings if it is more reliable.

22. Surface model selection inspector. Implemented January 8, 2008.
Tom Goddard
April 12, 2007
Make attribute inspector for surface models (volume, multiscale, ...) allow changing between mesh/filled, Have it report number of surface triangles.

21. Surface model, C++ to Python.
Tom Goddard
April 12, 2007
Convert surface model (_surface.Surface_Model) to Python leaving just speed critical rendering in C++. Will allow easier addition of new surface capabilities, and move alot of non-speed critical C++ code to easier to maintain Python code. Incorporate geometry changed callbacks in new model.

20. Distribute Python modules separate from Chimera.
Tom Goddard
April 12, 2007
Package contouring, capping and other independent volume tools as separate python modules and distribute separately on web.

19. Splitting volumes.
Tom Goddard
April 12, 2007
Make tools for slicing volume along a plane and enable moving of resulting two pieces. Might move them apart some as soon as sliced. Make them selectable and allow move selection mouse mode to work on them. Want slice undo, or maybe rejoin command. To find place of desired cut might want to split open and then be able to move split point interactively.

18. Mask map to icosahedron. Prototype surface masking October 17, 2007
Wen Jiang, Gabe Lander
April 12, 2007
Mask volume to within icosahedron tool surface. Used for virus maps.

17. Masking within any surface. Prototype surface masking October 17, 2007
Tom Goddard
April 12, 2007
Zero volume outside an arbitrary surface. Or clip and cap a surface against a second closed surface. Use for icosahedral sphere clipping of virus maps.

16. Volume solid rendering improvements. New transparency blending August 2, 2007
Sebastian Haase
April 12, 2007
Normalize brightness so it does not vary with step size. Add plane interpolation gui for higher quality rendering.

15. Feature tracking in volume time series.
John Sedat
April 12, 2007
Track many markers on chromosomes in volume time series. Maybe look at minimal mass motion interpolation.

14. Determine map symmetries. Fit map prints rotation axis/angle/shift February 28, 2007
Tom Goddard
April 12, 2007
Use map fit to itself to interactively determine map symmetries. Those symmetries could be used in multiscale or with symcopies command to make multimers from a PDB monomer.

13. EMDB / PDB fitting.
Richard Newman, Cathy Lawson
April 12, 2007
Find correct alignments of all PDB models fit in EMDB maps and have EMDB provide the transformation matrices in their XML meta data files to display those alignments. Allow Chimera to fetch models and maps using XML meta data file and show fit.

12. Record model motions.
Gali Golan
April 12, 2007
Make a trajectory recorder for models and pieces of models for movie making.

11. Put old plugins on web. Volume stats distributed October 3, 2007
Tom Goddard
April 12, 2007
Add to experimental features page: volume statistics, export obj, and nanoscope file reader.

10. Chimera web page for electron microscopy.
Tom Goddard
April 12, 2007
Make Chimera EM home page with links to EM features, examples, tutorials.

9. APBS documentation.
Tom Goddard
April 12, 2007
Write howto for computing electrostatic potential with APBS.

8. Surface cap triangulation.
Tom Goddard
April 12, 2007
Make regular hexagonal triangulation of surface caps with stitching of boundary. Provide better quality per-vertex cap coloring. Avoid triangulation artifacts seen capping Heather McCunes chromosome em map. This may be algorithmically too difficult.

7. Surface smoothing. Fixed by using gradient normals, October 6, 2007
Tom Goddard, Steve Ludtke
April 12, 2007
Find smoothing algorithm to eliminate surface smoothing pimples seen in volume contour surfaces and multiscale surfaces.

6. Defining multiscale hierarchy.
Tom Goddard
April 12, 2007
Add basic grouping / ungrouping capabilities to multiscale. Allow surfacing groups. Would like to be able to divide 23S rRNA single chain into multiple pieces. Want to be able to group pentamers of virus capsid as single pieces.

5. Surface display optimization. Implemented June 6, 2008.
Tom Goddard
April 12, 2007
Try opengl vertex buffer objects for surface models to see if it is faster for first time display than display list compilation. Tests show display list compilation take 10-100x longer than single direct rendering pass. VBO should be as fast as direct rendering for first draw, and as fast as display list for subsequent redraws.

4. Ellipsoid molecule display.
Tom Goddard
April 12, 2007
Molecules or small complexes may be represented by ellipsoids. Match ellipsoids to inertia tensor out to specified radius. Don't currently have rendering for ellipsoids -- can't use atoms unless atom objects enhanced.

3. Fetch by ID save button.
Tom Goddard
April 12, 2007
Have "Fetch & Save" button on Fetch by ID dialog to immediately save fetched file locally.

2. Fetch by ID database descriptions.
Tom Goddard
April 12, 2007
Have balloon help on database names in fetch by id dialog to explain the type of data available.

1. Fetch EDS maps. Implemented April 27, 2007
Tom Goddard, forgot user
April 12, 2007
Provide mFo-DFc EDS crystallographic density maps from EDS from fetch by id dialog. Currently only can fetch 2mFo-DFc map.