Changes between Initial Version and Version 1 of requests

Timestamp:

Feb 10, 2009, 3:42:49 PM (17 years ago)

Author:

goddard

Comment:

--

requests

@@ +1 @@
+{{{
+#!html
+
+<h1>
+Chimera Requests and Ideas
+</h1>
+
+<p>
+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).
+</p>
+
+<p>
+162.
+<b>Difference map when fitting.</b><br>
+
+Paul Dreizen<br>
+Jan 6, 2009<br>
+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.
+</p>
+
+<p>
+161.
+<b>Add two volumes.</b><br>
+Martin Kampmann<br>
+Dec 9, 2008<br>
+Improve vop command to allow adding two volumes with differing grids.
+For example, "vop #0 add #1 extend true sample true multiplier 0.25".
+</p>
+
+<p>
+160.
+<b>Surface cappping command.</b><br>
+Gabe Lander<br>
+Sept 9, 2008<br>
+Make command to turn on/off surface capping.  Also to set color, style,
+subdivision of caps.
+</p>
+
+<p>
+159.
+<b>Handle volume series as a single data set.</b><br>
+Sebastian Haase<br>
+
+July 21, 2008<br>
+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.
+</p>
+
+<p>
+158.
+<b>Add origin parameter to
+<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html">shape</a> command.</b>
+<font color=green>Implemented October 17, 2008</font><br>
+Ed Brignole, Elaine Meng<br>
+July 17, 2008<br>
+
+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.
+</p>
+
+<p>
+157.
+<b><a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html">Turn</a>
+command center of rotation argument.</b>
+<font color=green>Implemented October 17, 2008</font><br>
+Haixin Sui<br>
+July 15, 2008<br>
+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.
+</p>
+
+<p>
+156.
+<b>Volume rotation in Euler angles.</b><br>
+Haixin Sui<br>
+July 15, 2008<br>
+Allow volume rotation of local coordinates to be specified in Euler angles.
+Currently must be specified axis vector and rotation angle.
+</p>
+
+<p>
+155.
+<b>Volume origin in index units.</b>
+<font color=green>Implemented September 9, 2008</font><br>
+
+Haixin Sui<br>
+July 15, 2008<br>
+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.
+</p>
+
+<p>
+154.
+<b>Create PDB copies covering map.</b><br>
+Christian<br>
+July 15, 2008<br>
+Use crystal symmetry to create copies of PDB model to cover all density
+in an x-ray map.
+</p>
+
+<p>
+153.
+<b>Crystal map sigma units.</b><br>
+Terry Lang, several others<br>
+July 15, 2008<br>
+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.
+</p>
+
+<p>
+152.
+<b>Periodic covering map command.</b><br>
+Terry Lang<br>
+
+July 15, 2008<br>
+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).
+</p>
+
+<p>
+151.
+<b>Tile newly opened models.</b><br>
+Eduardo Sanz Garcia<br>
+July 3, 2008<br>
+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.
+</p>
+
+<p>
+
+150.
+<b>Space Navigator on Linux.</b><br>
+D Greening<br>
+July 14, 2008<br>
+Want space navigator support on Linux.
+</p>
+
+<p>
+149.
+<b>Place markers on surfaces.</b><br>
+Daniel Hautzinger<br>
+July 11, 2008<br>
+
+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.
+</p>
+
+<p>
+148.
+<b>Pipes and planks coloring.</b><br>
+Gary Ren<br>
+June 26, 2008<br>
+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.
+</p>
+
+<p>
+147.
+<b>Calculate difference map.</b>
+
+<font color=green>Implemented June 18, 2008</font><br>
+Jean-Paul Armache<br>
+June 2, 2008<br>
+Want to subtract two maps that have identical grids.  Could be added to
+"vop" command.
+</p>
+
+<p>
+146.
+<b>Add torus to shape command.</b><br>
+Pradeep Pallan<br>
+May 12, 2008<br>
+
+Want to show a circle to indicate size of a molecular structure.
+</p>
+
+<p>
+145.
+<b>Don't include hidden surface in area/volume.</b><br>
+Ed Brignole<br>
+May 12, 2008<br>
+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.
+</p>
+
+<p>
+144.
+<b>Report area/volume in volume dialog.</b><br>
+
+Ed Brignole<br>
+May 12, 2008<br>
+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.
+</p>
+
+<p>
+143.
+<b>Command for running keyboard shortcuts.</b>
+<font color=green>Implemented April 8, 2008</font><br>
+Jean-Didier Marechal.<br>
+March 27, 2008<br>
+
+Would like a command for running a keyboard shortcut.  Makes shortcut
+capabilities easily accessible from a script.  Could extend "ac" command.
+</p>
+
+<p>
+142.
+<b>Enable shortcuts for volume eraser.</b><br>
+Weimin Wu.<br>
+March 26, 2008<br>
+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.
+</p>
+
+<p>
+141.
+<b>Optimize volume grid spacing to best fit a molecule.</b><br>
+
+Stefan Backstrom.<br>
+March 26, 2008<br>
+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.
+</p>
+
+<p>
+140.
+<b>Fit molecules in map avoiding steric clashes.</b><br>
+Andrea Rossi.<br>
+March 13, 2008<br>
+In low density map, place one molecule and locally optimize the fit another
+without causing clashes with those already placed.
+</p>
+
+<p>
+139.
+<b>Volume eraser undo.</b><br>
+Htet Khant.<br>
+March 11, 2008<br>
+Undo button on volume eraser dialog to avoid having to save map frequently.
+</p>
+
+<p>
+138.
+<b>Add per-model clip command "frames" argument.</b><br>
+Eric Pettersen.<br>
+
+February 22, 2008<br>
+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...
+</p>
+
+<p>
+137.
+<b>Two per-model clip planes for wedges.</b><br>
+Tom Goddard.<br>
+February 14, 2008<br>
+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.
+</p>
+
+<p>
+
+136.
+<b>Less sensitive solid volume brightness / transparency.</b>
+<font color=green>Implemented February 15, 2008</font><br>
+Jeff Triffo.<br>
+February 14, 2008<br>
+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.
+</p>
+
+<p>
+135.
+<b>Angle dependent transparency.</b><br>
+Andrew Jewett.<br>
+
+February 14, 2008<br>
+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.
+</p>
+
+<p>
+134.
+<b>Output volume solid brightness curve.</b><br>
+Jeff Triffo.<br>
+February 14, 2008<br>
+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.
+</p>
+
+<p>
+133.
+<b>Color by atom on surface caps.</b><br>
+Elaine Meng.<br>
+February 14, 2008<br>
+Colors surface caps of molecular surfaces by nearby atom colors.
+</p>
+
+<p>
+132.
+<b>Make capping on by default for per-model clip planes.</b>
+<font color=green>Implemented November 4, 2008</font><br>
+
+Tom Goddard.<br>
+February 8, 2008<br>
+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, ....
+</p>
+
+<p>
+131.
+<b>Different colors for surface inside and outside.</b><br>
+Ian Yarbrough.<br>
+February 4, 2008<br>
+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.
+</p>
+
+<p>
+130.
+<b>Make crytal map and PDB model coincide.</b>
+<font color=green>Implemented Nov 20, 2007. Keyboard shortcut "bv" creates covering map.</font><br>
+Trevor Sewell, Terry Lang.<br>
+February 4, 2008<br>
+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.
+</p>
+
+<p>
+129.
+<b>Read brix maps as 8-bit values.</b><br>
+
+Thomas Becker.<br>
+February 4, 2008<br>
+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.
+</p>
+
+<p>
+128.
+<b>Surface transparency with color zone.</b><br>
+James Fethiere.<br>
+January 30, 2008<br>
+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.
+</p>
+
+<p>
+127.
+<b>Label unit cell axes and show cell offset.</b><br>
+Dirk Kostrewa.<br>
+January 30, 2008<br>
+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).
+</p>
+
+<p>
+126.
+<b>Place markers on any visible volume.</b><br>
+C Akey.<br>
+
+January 25, 2008<br>
+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.
+</p>
+
+<p>
+125.
+<b>RGB TIFF image file reader.</b><br>
+Sebastian Haase.<br>
+January 23, 2008<br>
+Read RGB tiff image files as 3 scalar volume data sets.
+</p>
+
+<p>
+
+124.
+<b>Extend map using symmetry.</b><br>
+Francesco Zonta.<br>
+January 18, 2008<br>
+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
+<a href="http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_6.html#SEC146">this</a>.
+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.
+</p>
+
+<p>
+123.
+<b>Color using MolMol electrostatic potential.</b><br>
+Esther Bullitt.<br>
+
+January 16, 2008<br>
+Read MolMol electrostatic potential grid data for coloring molecular
+surfaces.  Format is very simple and is described in MolMol ReadPot manual
+page.
+</p>
+
+<p>
+122.
+<b>Multi-page TIFF image file reader.</b>
+<font color=green>Implemented January 22, 2008</font><br><br>
+Sebastian Haase.<br>
+January 15, 2008<br>
+Read multipage tiff image files as volume data.  Sebastian provided example
+Python code for reading such files.
+</p>
+
+<p>
+121.
+<b>Correlation for fitting model in map.</b>
+<font color=green>Implemented February 21, 2008</font><br>
+C Akey.<br>
+January 14, 2008<br>
+Use cross-correlation coefficient to fit atomic model in map.  Will require
+making simulated map at target map resolution.
+</p>
+
+<p>
+120.
+<b>Area/volume command.</b><br>
+
+Zhiya Sheng.<br>
+December 26, 2007<br>
+Make a command for reporting surface area and enclosed volume.
+</p>
+
+<p>
+119.
+<b>Crystal lattice command.</b><br>
+Jack Johnson.<br>
+December 20, 2007<br>
+Make a command to create copies of atomic models to fill a crystal lattice.
+</p>
+
+<p>
+118.
+<b>Icoshedron mesh command.</b>
+<font color=green>Implemented January 24, 2008
+(<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html">shape</a> command).</font><br>
+Jack Johnson.<br>
+December 20, 2007<br>
+Make a command equivalent to the icosahedron surface tool.
+</p>
+
+<p>
+117.
+<b>Hide all models button.</b><br>
+Eduardo Sanz Garcia.<br>
+November 26, 2007<br>
+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.
+</p>
+
+<p>
+116.
+<b>Easy hiding of all but one volume.</b><br>
+Eduardo Sanz Garcia.<br>
+
+November 26, 2007<br>
+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.
+</p>
+
+
+<p>
+115.
+<b>Scrollbar for volume histogram panels.</b><br>
+Eduardo Sanz Garcia.<br>
+November 26, 2007<br>
+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.
+</p>
+
+<p>
+114.
+<b>Save color palettes.</b><br>
+Jeff Triffo.<br>
+November 26, 2007<br>
+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.
+</p>
+
+<p>
+113.
+<b>Animation extracting octant from virus density.</b><br>
+Yen-Chywan Liaw.<br>
+
+November 15, 2007<br>
+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.
+</p>
+
+<p>
+112.
+<b>Animation where ligand flies into bound state.</b><br>
+Yen-Chywan Liaw.<br>
+November 15, 2007<br>
+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.
+</p>
+
+<p>
+
+111.
+<b>Want easy way to morph both volume and pdb model.</b><br>
+Haixin Sui, Yen-Chywan Liaw.<br>
+November 15, 2007<br>
+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.
+</p>
+
+<p>
+110.
+<b>Reverse order of colors in
+<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html">surface color</a> tool.</b>
+
+<font color=green>Implemented April 17, 2008.</font><br>
+Yen-Chywan Liaw.<br>
+November 15, 2007<br>
+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.
+</p>
+
+<p>
+109.
+<b>Make POVray appearance better match Chimera window.</b><br>
+Ed Egelman, others.<br>
+November 15, 2007<br>
+
+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.
+</p>
+
+<p>
+108.
+<b>Set contour levels for multiple volumes at once.</b><br>
+Steve Ludtke.<br>
+November 15, 2007<br>
+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.
+</p>
+
+<p>
+107.
+<b>Set morph map contour level to preserve enclosed volume.</b><br>
+
+Pawel Penzcek.<br>
+November 15, 2007<br>
+Add option to preserve enclosed volume when using morph map.  Volume series
+tool already has this so some code is already available.
+</p>
+
+<p>
+106.
+<b>Read PRIISM format volume files with WZT disk layout.</b>
+<font color=green>Implemented June 3, 2008.</font><br>
+Sebastian Haase.<br>
+November 15, 2007<br>
+
+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.
+</p>
+
+<p>
+105.
+<b>Command to print relative model orientation.</b><br>
+Duncan Sousa.<br>
+November 13, 2007<br>
+Add command to print relative model orientation: rotation angle, axis, shift.
+Might support alternate formats like rotation matrix / shift.
+</p>
+
+<p>
+104.
+<b>Cubic volume interpolation.</b><br>
+
+Terry Lang.<br>
+October 23, 2007<br>
+Add cubic volume interpolation at points as alternative to trilinear
+interpolation.  Want this for searching for alternate side-chain
+conformations in x-ray maps.
+</p>
+
+<p>
+103.
+<b>Fit using correlation.</b><br>
+Alexander Solodukhin.<br>
+October 1, 2007<br>
+Fit map in map using correlation instead of overlap so that fit is not
+simply pushed to high density region with poorly matching shape.
+</p>
+
+<p>
+102.
+<b>Thick surfaces.</b><br>
+Jeff Triffo.<br>
+September 19, 2007<br>
+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.
+</p>
+
+<p>
+101.
+<b>IMOD session saving.</b><br>
+Jeff Triffo.<br>
+
+August 20, 2007<br>
+Want IMOD surfaces that have been recolored in Chimera saved in
+session files.
+</p>
+
+<p>
+100.
+<b>IMAGIC-5 volume file reader.</b><br>
+Michael Schatz.<br>
+July 13, 2007<br>
+Write volume file reader for the em2em native IMAGIC-5 file format.
+</p>
+
+<p>
+
+99.
+<b>Nintendo Wii controller for volume fly-through.</b>
+<font color=green>Tested with DarwiinRemote September 27, 2007</font><br>
+Dan Greenblatt.<br>
+July 10, 2007<br>
+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.
+</p>
+
+<p>
+98.
+<b>Contour surface, include box boundaries.</b>
+<font color=green>Implemented October 9, 2007</font><br>
+
+Tom Goddard.<br>
+July 3, 2007<br>
+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.
+</p>
+
+<p>
+97.
+<b>Volume fly-through controls.</b><br>
+Manfred Auer.<br>
+July 2, 2007<br>
+Allow fly through navigation controls for EM tomography data.
+Could use game controller input device.
+</p>
+
+<p>
+96.
+<b>Better error message when volume data too large.</b>
+<font color=green>Done August 23, 2007</font><br>
+Irina Serysheva, Matt Dougherty.<br>
+June 28, 2007<br>
+Provide a simple error message instead of a Python traceback when
+the memory allocation fails in reading a large volume array.
+</p>
+
+<p>
+95.
+<b>Color IMOD surfaces with Actions/Color menu.</b><br>
+
+Jeff Triffo.<br>
+June 28, 2007<br>
+Would like to be able to color selected IMOD surfaces with the Actions / Color
+menu.  Can use "co" keyboard shortcut currently.
+</p>
+
+<p>
+94.
+<b>Help buttons on volume viewer panels.</b><br>
+Elaine Meng.<br>
+June 4, 2007<br>
+Want "?" buttons next to the "x" buttons on volume viewer panels that show
+the appropriate subsection of the volume viewer user's guide page.
+</p>
+
+<p>
+93.
+<b>Simplify volume data Python calls.</b>
+<font color=green>Many improvements August 23, 2007</font><br>
+Gabor Papai.<br>
+May 24, 2007<br>
+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.
+</p>
+
+<p>
+92.
+<b>Make multiscale tool work when atoms deleted.</b>
+
+<font color=green>Implemented October 25, 2008.</font><br>
+Andy LiWang.<br>
+May 24, 2007<br>
+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.
+</p>
+
+<p>
+91.
+<b>Save image without Chimera window shown.</b><br>
+Jawahar Swaminathan (MSD).<br>
+May 24, 2007<br>
+
+Want to save Chimera images in nogui mode (no Chimera window shown)
+to make virus capsid images for Macromolecular Structure Database.
+</p>
+
+<p>
+90.
+<b>Display 2-d contour lines on clipped volume surfaces.</b>
+<font color=green>Implemented September 9, 2008</font><br>
+Yao Cong.<br>
+May 22, 2007<br>
+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.
+</p>
+<p>
+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.
+
+</p>
+
+<p>
+89.
+<b>Make experimental plugins check Chimera version compatibility.</b><br>
+Eric Pettersen.<br>
+May 22, 2007<br>
+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.
+</p>
+
+<p>
+88.
+<b>Show map standard deviation.</b>
+
+<font color=green>Menu entry to print mean/SD values October 10, 2007</font><br>
+Holland Cheng.<br>
+May 5, 2007<br>
+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.
+</p>
+
+<p>
+87.
+<b>Raw map file reader.</b><br>
+Request at UC Davis bay area cryoEM meeting.<br>
+May 5, 2007<br>
+
+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.
+</p>
+
+<p>
+86.
+<b>Amira segmentation file reader.</b><br>
+Request at UC Davis bay area cryoEM meeting.<br>
+May 5, 2007<br>
+Add file reader for Amira segementation files.
+</p>
+
+<p>
+85.
+<b>Fetch PDB biounit files.</b><br>
+
+Tom Goddard<br>
+April 23, 2007<br>
+Add fetch by id for PDB biounit files.
+</p>
+
+<p>
+84.
+<b>Thicker silhouette edges.</b>
+<font color=green>Done July 28, 2007</font><br>
+Tom Goddard<br>
+April 20, 2007<br>
+
+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
+<a href="http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/clathrin/clathrin.html">clathrin image gallery entry</a>
+illustrates a case where the thicker edges are desirable.  
+</p>
+
+<p>
+83.
+<b>Warn about ambiguous transforms.</b><br>
+Preethi Chandramouli, Tom Goddard<br>
+April 19, 2007<br>
+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.
+</p>
+
+<p>
+82.
+<b>2-d overlays and labels on molecular surfaces.</b><br>
+Tom Goddard<br>
+April 18, 2007<br>
+Add ability to draw residue outlines and residue text labels on molecular
+surfaces as illustrated in
+<ul>
+<li>
+Xiao C, Rossmann MG.<br>
+Interpretation of electron density with stereographic roadmap projections.<br>
+J Struct Biol. 2006 Oct 24; [Epub ahead of print]
+</ul>
+
+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.
+</p>
+
+<p>
+81.
+<b>Calculate density map for molecule.</b>
+<font color=green>Implemented January 14, 2008.</font><br>
+Thomas Marlovits<br>
+April 17, 2007<br>
+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.
+</p>
+
+<p>
+
+80.
+<b>Trace protein backbone.</b><br>
+Matthew Baker<br>
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+79.
+<b>Multiple graphics windows.</b><br>
+Xiaoyun Chen<br>
+April 12, 2007<br>
+
+Want separate graphics windows for three orthogonal views: xy, yz and xz.
+</p>
+
+<p>
+78.
+<b>Path tracer markers.</b><br>
+Eric Pettersen<br>
+April 12, 2007<br>
+Put each path tracer marker in a separate residue to allow commands that use
+residue numbers to handle consecutive series of markers.
+</p>
+
+<p>
+77.
+<b>Path tracer marker attributes.</b><br>
+
+Jeff Triffo<br>
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+76.
+<b>Fetch EMDB maps.</b><br>
+Cathy Lawson<br>
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+75.
+<b>Fetch PQS biological assemblies.</b>
+<font color=green>Implemented April 27, 2007</font><br>
+
+Miguel Ortiz Lombardia<br>
+April 12, 2007<br>
+Add PQS biological assembly files (*.mmol) to fetch by id.
+</p>
+
+<p>
+74.
+
+<b>Volume rendering size limit.</b><br>
+Tom Goddard<br>
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+73.
+<b>Color surface pieces.</b><br>
+Anindito Sen<br>
+April 12, 2007<br>
+
+Make pick surface pieces surface coloring save in session files.
+</p>
+
+<p>
+72.
+<b>Biological assemblies in mmcif.</b><br>
+Cathy Lawson<br>
+April 12, 2007<br>
+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'
+</p>
+
+<p>
+71.
+<b>Reoriented density maps.</b>
+
+<font color=green>Done for MRC and HDF formats September 4, 2007</font><br>
+Tom Goddard<br>
+April 12, 2007<br>
+Include rotation in written map header when resampled piece of volume
+extracted with addmaps command.
+</p>
+
+<p>
+70.
+<b>Subsample volume data, netcdf.</b>
+<font color=green>Done with HDF, netcdf deprecated September 11, 2007</font><br>
+Matt Baker<br>
+
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+69.
+<b>HDF map file reader.</b>
+<font color=green>Done August 7, 2007</font><br>
+Matt Dougherty, Pawel Penczek<br>
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+68.
+<b>Radial density plot.</b>
+<font color=green>Made radial density calculation script March 2, 2007</font><br>
+Padma Natarajan<br>
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+67.
+<b>Setting figure magnification.</b><br>
+
+Christopher Akey<br>
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+66.
+<b>Save BRIX format.</b>
+<font color=green>Added prototype BRIX writer October 19, 2007</font><br>
+Christopher Akey<br>
+April 12, 2007<br>
+
+Write maps in BRIX format.  This is for interoperation with O for building
+models in EM maps.
+</p>
+
+<p>
+65.
+<b>User-defined surfaces.</b>
+<font color=green>Implemented January 30, 2008.</font><br>
+Jeff Triffo<br>
+April 12, 2007<br>
+Create surface from volume path tracer markers.  Used for electron tomography
+annotation.
+</p>
+
+<p>
+
+64.
+<b>Save more EM map file formats.</b>
+Christos Gatsogiannis<br>
+April 12, 2007<br>
+Write additional volume file formats (situs, imagic).
+</p>
+
+<p>
+63.
+<b>Arrows on morphed maps.</b><br>
+Tom Goddard<br>
+April 12, 2007<br>
+
+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.
+</p>
+
+<p>
+62.
+<b>Volume viewer code clean-up.</b>
+<font color=green>Done August 9, 2007</font><br>
+Tom Goddard<br>
+April 12, 2007<br>
+Simplify volume viewer code by using Checkbutton_Entries from Hybrid.py.
+</p>
+
+<p>
+
+61.
+<b>Benchmark scores.</b>
+<font color=green>Implemented May 2, 2008.</font><br>
+Tom Goddard<br>
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+60.
+<b>Color zone slider range.</b>
+<font color=green>Implemented October 3, 2007.</font><br>
+
+Jeff Triffo<br>
+April 12, 2007<br>
+Make color zone set the maximum slider value based on the diameter of the
+displayed surface.
+</p>
+
+<p>
+59.
+<b>Copying volume display settings.</b><br>
+Jeff Triffo<br>
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+58.
+<b>Map plane display.</b><br>
+Jeff Triffo<br>
+April 12, 2007<br>
+Allow averaging together neighboring planes in em tomography when displaying
+a single slice to improve signal to noise.
+</p>
+
+<p>
+57.
+<b>Slicing EM maps.</b>
+<font color=green>Resample volume added September 4, 2007</font><br>
+
+Jeff Triffo<br>
+April 12, 2007<br>
+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.
+<a href="http://tigertiger.de/cb/research-chimera.html">Web site.</a>
+</p>
+
+<p>
+56.
+<b>Volume zones, solid rendering.</b><br>
+Jeff Triffo<br>
+April 12, 2007<br>
+
+Make volume zones work in solid display mode.
+</p>
+
+<p>
+55.
+<b>Save marker sets relative to models.</b><br>
+Heather McCune<br>
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+54.
+<b>Volume rendering memory use.</b>
+
+<font color=green>Implemented September 6, 2008.</font><br>
+Tom Goddard<br>
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+53.
+<b>Clip plane motion user interface.</b><br>
+Jeff Triffo<br>
+April 12, 2007<br>
+
+Make buttons and sliders to control perpendicular axis and translation of
+per-model clip planes for volume data.
+</p>
+
+<p>
+52.
+<b>Update graphics driver bugs web page.</b><br>
+Tom Goddard<br>
+April 12, 2007<br>
+Search closed chimera bugs for graphics driver issues and add them to the
+graphics driver bug page.
+</p>
+
+<p>
+51.
+<b>Crystal contacting chains.</b>
+
+<font color=green>Partially done October 10, 2007
+(<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/crystalcontacts/crystalcontacts.html">crystal contacts</a> tool).</font><br>
+Miguel Ortiz-Lombardia<br>
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+50.
+<b>Atomic force microscope file reader.</b><br>
+Alberto Roca<br>
+
+April 12, 2007<br>
+Put nanoscope AFM tools on experimental features page.  Will need
+documentation. 
+</p>
+
+<p>
+49.
+<b>Unit cell outline box.</b><br>
+<font color=green>Meshmol command can serve October 10, 2007</font><br>
+Sabuj Pattanayek<br>
+April 12, 2007<br>
+Add unit cell outline box color and line thickness controls to Unit Cell
+dialog.
+</p>
+
+<p>
+48.
+<b>Contouring optimization.</b>
+<font color=green>New optimized algorithm October 2, 2007</font><br>
+Tom Goddard<br>
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+47.
+<b>Volume subsample voxel origin.</b><br>
+
+Tom Goddard<br>
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+46.
+<b>Multiple volume dialogs.</b>
+<font color=green>Multiple volume histograms added August 10, 2007</font><br>
+Basal Devkota<br>
+April 12, 2007<br>
+
+Allow two or more volume viewer dialogs for adjusting multiple maps easily.
+</p>
+
+<p>
+45.
+<b>XYZ axis display.</b><br>
+Jeff Triffo, Haixin Sui<br>
+April 12, 2007<br>
+Add a tool to make axes arrows using BILD, ala VMD to indicate orientation.
+</p>
+
+<p>
+44.
+<b>Better multiscale surface quality.</b><br>
+
+Tom Goddard<br>
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+43.
+<b>Reading large maps.</b>
+<font color=green>Done July 31, 2007</font><br>
+Irina Serysheva<br>
+April 12, 2007<br>
+
+Make volume subsampling not allocate unsubsampled array when reading from
+file.  Limits reading of large data sets.
+</p>
+
+<p>
+42.
+<b>Collaboration descriptions.</b><br>
+Tom Goddard<br>
+April 12, 2007<br>
+Add VIPERdb and EMDB collaboration web pages to CGL Research index.
+</p>
+
+<p>
+41.
+<b>Measure enclosed volume.</b>
+
+<font color=green>Added keyboard shortcuts mv and ma September 29, 2006</font><br>
+Tom Goddard<br>
+April 12, 2007<br>
+Add option to measure volume/area to only measure selected surfaces.
+</p>
+
+<p>
+40.
+<b>Icosahedron surface session saving.</b>
+<font color=green>Added December 5, 2008</font><br>
+Tom Goddard<br>
+
+April 12, 2007<br>
+Add session saving to icosahedron tool.
+</p>
+
+<p>
+39.
+<b>IMOD file reader.</b>
+<font color=green>Added to distribution October 5, 2007</font><br>
+Masako Terada<br>
+April 12, 2007<br>
+Put IMOD segmentation surface file reader in Chimera distribution.
+</p>
+
+<p>
+38.
+<b>Image sequence file reader.</b>
+<font color=green>Added TIFF stack reader July 21, 2007</font><br>
+William Beaver<br>
+April 12, 2007<br>
+Add image sequence (tiff, pnm) volume file reader.
+</p>
+
+<p>
+37.
+<b>Color zone with multiple radii.</b><br>
+
+Hernando Sosa<br>
+April 12, 2007<br>
+Consider allowing sequences of colorings in color zone.  Would allow using
+multiple radii.  Also greater flexibility in coloring.
+</p>
+
+<p>
+36.
+<b>Make chains become separate molecules.</b>
+<font color=green>Added to distribution October 10, 2007</font><br>
+Elaine Meng<br>
+April 12, 2007<br>
+
+Add split molecule command to Chimera distribution.  Makes each chain a
+separate molecule.  Currently on experimental features web page.
+<a href="http://www.cgl.ucsf.edu/chimera/experimental/split_molecule/split.html">split</a>.
+</p>
+
+<p>
+35.
+<b>Delphi Controller surface coloring.</b>
+<font color=green>Implemented April 25, 2007.</font><br>
+Elaine Meng<br>
+April 12, 2007<br>
+Make DelphiController show potential on MSMS surface with Surface Color tool.
+Currently potential is shown with volume viewer.
+</p>
+
+<p>
+34.
+<b>Print map values.</b><br>
+Nihshanka Debroy<br>
+April 12, 2007<br>
+Allow clicking on a surface to print volume value at the corresponding surface
+point, for example electrostatic potential.
+</p>
+
+<p>
+33.
+<b>Surface coloring key.</b>
+<font color=green>Implemented July 15, 2008.</font><br>
+
+Alexander Rusnak<br>
+April 12, 2007<br>
+Add color key to surface color tool using surface strip.
+</p>
+
+<p>
+32.
+<b>Movie recorder format compatibility.</b>
+<font color=green>Powerpoint movie fixes documented March 2, 2007</font><br>
+Tom Goddard<br>
+April 12, 2007<br>
+
+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.
+</p>
+
+<p>
+31.
+<b>Switching volume dialog volume.</b><br>
+Jean-Francois Menetret<br>
+April 12, 2007<br>
+Have volume viewer automatically switch to show most recently displayed
+volume (switched perhaps in Model Panel) in volume dialog.
+</p>
+
+<p>
+30.
+<b>Volume commands for movies.</b><br>
+
+Frank Albers, Jeff Triffo<br>
+April 12, 2007<br>
+Want volume commands for making animations.  Wants color fades.
+Want per-model clip plane transitions.
+</p>
+
+<p>
+29.
+<b>Volume bit masks.</b><br>
+Tom Goddard<br>
+April 12, 2007<br>
+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, ....
+</p>
+
+<p>
+28.
+<b>Mask volume with cylinder.</b>
+<font color=green>Implemented October 17, 2007
+(<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html">mask</a>
+and
+<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html">shape</a>
+commands).</font><br>
+Haixin Sui<br>
+April 12, 2007<br>
+
+Masking density to cylinders, masking with an external mask file.
+Used for cylindrical virus particles.
+</p>
+
+<p>
+27.
+<b>Fit selected atoms in map.</b><br>
+Several users<br>
+April 12, 2007<br>
+Add option to fit model in map tool to move only selected atoms.
+</p>
+
+<p>
+26.
+<b>Buried surface area.</b><br>
+
+Tom Goddard<br>
+April 12, 2007<br>
+Tool to report buried surface areas between two chains, between 1 chain and
+all contacting chains, or between all pairs of contacting chains.
+</p>
+
+<p>
+25.
+<b>Multiscale chain coloring.</b><br>
+Tom Goddard<br>
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+24.
+<b>Electrostatic potential coloring.</b>
+<font color=green>Similar fix made May 6, 2008.</font><br>
+Elaine Meng<br>
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+23.
+<b>MSMS surface calculation with stand-alone program.</b>
+
+<font color=green>Implemented March 18, 2008.</font><br>
+Tom Goddard<br>
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+22.
+<b>Surface model selection inspector.</b>
+<font color=green>Implemented January 8, 2008.</font><br>
+Tom Goddard<br>
+
+April 12, 2007<br>
+Make attribute inspector for surface models (volume, multiscale, ...)
+allow changing between mesh/filled,  Have it report number of surface triangles.
+</p>
+
+<p>
+21.
+<b>Surface model, C++ to Python.</b><br>
+Tom Goddard<br>
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+
+20.
+<b>Distribute Python modules separate from Chimera.</b><br>
+Tom Goddard<br>
+April 12, 2007<br>
+Package contouring, capping and other independent volume tools as separate
+python modules and distribute separately on web.
+</p>
+
+<p>
+19.
+<b>Splitting volumes.</b><br>
+Tom Goddard<br>
+April 12, 2007<br>
+
+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.
+</p>
+
+<p>
+18.
+<b>Mask map to icosahedron.</b>
+<font color=green>Prototype surface masking October 17, 2007</font><br>
+Wen Jiang, Gabe Lander<br>
+April 12, 2007<br>
+Mask volume to within icosahedron tool surface.  Used for virus maps.
+</p>
+
+<p>
+
+17.
+<b>Masking within any surface.</b>
+<font color=green>Prototype surface masking October 17, 2007</font><br>
+Tom Goddard<br>
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+16.
+<b>Volume solid rendering improvements.</b>
+<font color=green>New transparency blending August 2, 2007</font><br>
+
+Sebastian Haase<br>
+April 12, 2007<br>
+Normalize brightness so it does not vary with step size.
+Add plane interpolation gui for higher quality rendering.
+</p>
+
+<p>
+15.
+<b>Feature tracking in volume time series.</b><br>
+John Sedat<br>
+April 12, 2007<br>
+Track many markers on chromosomes in volume time series.
+Maybe look at minimal mass motion interpolation.
+</p>
+
+<p>
+14.
+<b>Determine map symmetries.</b>
+<font color=green>Fit map prints rotation axis/angle/shift February 28, 2007</font><br>
+Tom Goddard<br>
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+13.
+<b>EMDB / PDB fitting.</b><br>
+
+Richard Newman, Cathy Lawson<br>
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+12.
+<b>Record model motions.</b><br>
+Gali Golan<br>
+April 12, 2007<br>
+Make a trajectory recorder for models and pieces of models for movie making.
+</p>
+
+<p>
+11.
+<b>Put old plugins on web.</b>
+<font color=green>Volume stats distributed October 3, 2007</font><br>
+Tom Goddard<br>
+April 12, 2007<br>
+Add to experimental features page: volume statistics, export obj, and
+nanoscope file reader.
+</p>
+
+<p>
+10.
+<b>Chimera web page for electron microscopy.</b><br>
+
+Tom Goddard<br>
+April 12, 2007<br>
+Make Chimera EM home page with links to EM features, examples, tutorials.
+</p>
+
+<p>
+9.
+<b>APBS documentation.</b><br>
+Tom Goddard<br>
+April 12, 2007<br>
+Write howto for computing electrostatic potential with APBS.
+</p>
+
+<p>
+8.
+<b>Surface cap triangulation.</b><br>
+Tom Goddard<br>
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+7.
+<b>Surface smoothing.</b>
+<font color=green>Fixed by using gradient normals, October 6, 2007</font><br>
+
+Tom Goddard, Steve Ludtke<br>
+April 12, 2007<br>
+Find smoothing algorithm to eliminate surface smoothing pimples seen in
+volume contour surfaces and multiscale surfaces.
+</p>
+
+<p>
+6.
+<b>Defining multiscale hierarchy.</b><br>
+Tom Goddard<br>
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+5.
+<b>Surface display optimization.</b>
+<font color=green>Implemented June 6, 2008.</font><br>
+Tom Goddard<br>
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+4.
+<b>Ellipsoid molecule display.</b><br>
+
+Tom Goddard<br>
+April 12, 2007<br>
+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.
+</p>
+
+<p>
+3.
+<b>Fetch by ID save button.</b><br>
+Tom Goddard<br>
+April 12, 2007<br>
+Have "Fetch & Save" button on Fetch by ID dialog to immediately save
+fetched file locally.
+
+</p>
+
+<p>
+2.
+<b>Fetch by ID database descriptions.</b><br>
+Tom Goddard<br>
+April 12, 2007<br>
+Have balloon help on database names in fetch by id dialog to explain the
+type of data available.  
+</p>
+
+<p>
+1.
+<b>Fetch EDS maps.</b>
+
+<font color=green>Implemented April 27, 2007</font><br>
+Tom Goddard, forgot user<br>
+April 12, 2007<br>
+Provide mFo-DFc EDS crystallographic density maps from EDS from fetch by id
+dialog.  Currently only can fetch 2mFo-DFc map.
+</p>
+
+}}}