Chimera Requests and Ideas

This page lists ideas for new Chimera features and new documentation.

For recently implemented enhancements see the change log.

Component: Amber (3 matches)

Ticket	Summary	Priority	Milestone
#10806	allow custom leaprc files in Amber tools	normal
#10926	command version of Add Ions	normal
#7679	integration of Python-callable minimization	low
Component: Animate (20 matches)
Ticket	Summary	Priority	Milestone
#9055	Animate: define midas commands for animation	high	Release 1.8
#9336	Add per-model transition parameters	normal	Release 1.8
#9404	Animate Collaboration	normal	Release 1.8
#9441	Create 3D movies	normal
#9447	Movie preferences - integration	normal
#9805	Make Chimera produce streaming QuickTime movies	normal
#9812	Export movies in WebM format for playback in modern web browsers	normal
#9933	Make wait command work with all multiple frame commands	normal
#10045	Support video vp8 and h264 for use with HTML5	normal
#10115	Animation development ideas	normal
#10303	Scenes do not save Marker_Sets	normal	Release 1.8
#10304	Scene does not save multiscale model	normal	Release 1.8
#10442	Movie log file with frame numbers	normal	Release 1.8
#10443	Button to clear command-line	normal	Release 1.8
#10444	Button command-shortcuts	normal	Release 1.8
#11898	need easy way to apply overall effects to all scenes at once	normal	Release 1.8
#12856	Scenes not saving background image	normal	Release 1.11
#9515	Animate: use chimera.help.register	low	Release 1.8
#9500	Animate: Add selections to saved state	lowest	Release 1.8
#9679	Animate: animate background attributes	lowest	Release 1.8
Component: Core (48 matches)
Ticket	Summary	Priority	Milestone
#1351	balloon atomspec over surface should be more informative	high	none
#249	clipped-sphere "caps"	normal
#261	bond rotations in large complexes slow	normal
#539	atom deletion slow	normal
#3334	Want LensViewer.pilImage() for backwards compatibility.	normal
#3919	more graphics options control	normal
#4486	Want to set molecule xform before it is opened	normal
#6680	depict bond orders graphically	normal
#6819	undo capability	normal	none
#6888	better default new-dialog position	normal
#7010	Atom / Bond color methods using color hierarchy.	normal	none
#7535	Allow image save in --nogui mode.	normal
#7555	RFE: incorporate offset functionality into an existing command rather than standalone commands	normal	none
#7633	Allow hiding atom labels without losing custom label text	normal
#8027	Automated checkpoint session saving	normal
#9785	allow multiple attachments to bug reports	normal
#9800	new Chimera check in separate thread?	normal
#9845	Define a global coordinate system	normal
#9846	Make front center rotation more predictable	normal
#9852	Add a Chimera command shell	normal
#9906	Use SPDX to track licenses	normal
#10071	Want multiply operator for Xforms.	normal
#10223	better error handling for bug-report dialog	normal
#10344	Inter-residue bond selection is quirky	normal
#10629	"ordered" residues not ordered	normal
#10933	open "close existing session" when restoring session	normal
#10956	survey PDB for IDATM cutoff values	normal
#10961	"description" model attribute	normal
#10966	better comma handling in OSLs	normal
#10987	'isChemical' boolean in Molecule	normal
#11640	Make map C++ code accept 64-bit integer arrays on 64-bit Windows	normal
#11815	Simplify molecule coordinate systems	normal	Release 2.0
#12346	confirm-overwrite pref for savepos	normal
#3590	more info about "missing structure" pseudobonds	low
#7081	per-frame data	low
#8026	browsable session thumbnails/descriptions	low
#8352	third-party error reporting	low
#9594	flag chain-connectivity bonds	low
#10844	automatic session versioning	low
#11050	mention getting current version in bug-reporting dialog	low
#11062	doExtensionFunc: custom arg-conversion func	low
#8028	automated session versioning	lowest
#11077	use standard dialog for "Really Quit?"	lowest
#11081	make mol.primaryAtoms() return consistent set of locations	lowest
#11088	don't permanently clear logged status messages	lowest
#11090	find best atom ratio for 'ligand' categorization	lowest
#11097	identify protein/nucleic acids residues via connectivity	lowest
#11123	handle ambiguous atom names in residue templates	lowest
Component: Depiction (26 matches)
Ticket	Summary	Priority	Milestone
#1179	Would like smooth ribbon color transitions	normal
#1653	RFE: selectable per-atom surface	normal
#7879	rainbow on selection	normal
#8009	add multisampled frame buffer object support	normal	none
#8218	control of ring fill color	normal
#10952	better initial model setting for per-model clipping	normal
#10964	allow rainbow command/gui to color just ribbons or atoms	normal
#10967	'tint' coloring action	normal
#10992	"licorice" depiction available as standard action	normal
#11470	new-molecule color palettes/color wells/schemes	normal
#12062	Depict model axes	normal
#12813	RFE ability to mass-delete ribbon styles	normal
#16349	Feature request - custom color palettes in surface color	normal
#16760	RFE: update povray	normal
#10755	RFE: make "dumbbell" ribbon style (cross-section)	low
#11039	controller for # of wells in rainbow GUI	low
#11053	combine atom/bond draw modes in New Molecule prefs	low
#11057	"restrict to selection" for Color By SS	low
#11058	undo display states	low
#12099	"open" command to make pseudobond	low
#11073	chain-trace alternative that only follows the backbone	lowest
#11086	control over initial distance-monitor settings	lowest
#11104	rainbow by chain: skip ligand peptide chains	lowest
#11113	generate MolScript input	lowest
#11114	per-model clipping: session support	lowest
#11121	UI for stub bond control	lowest
Component: Documentation (2 matches)
Ticket	Summary	Priority	Milestone
#9827	Chimera Python API documentation	normal
#7533	generate programmer's reference guide	low
Component: General Controls (56 matches)
Ticket	Summary	Priority	Milestone
#16417	Use alt key to emulate middle mouse with trackpad on Windows laptops	high
#1721	Want command to set camera zoom	normal
#6874	grouping mechanism	normal
#7286	RFE: "set" keywords for 3D label control	normal
#7297	Open/Save: horizontal mouse-ball scroll should scroll all columns	normal
#7338	add windows menu	normal	none
#7900	incremental stereo controls	normal	none
#10404	RFE: context menus over Model Panel	normal	Release 2.0
#10507	camera tool improvements	normal	Release 2.0
#10922	order alias menu chronologically	normal
#10928	setattr 'note' -> show in model panel	normal
#10934	named-selection GUI	normal
#10937	'delete' keyword for ~setattr to delete attribute	normal
#10941	put "reset list" output all on one line	normal
#10942	ability to close command-line widget	normal
#10943	set preferences by command	normal
#10944	"updatepos" command for updating saved position with new models	normal
#10945	deprecate objdisplay command	normal
#10946	command to list attributes	normal
#10955	have initial Model Panel size show all columns	normal
#10962	labelopt precision	normal
#10969	better behavior for actions if only bonds selected	normal
#10974	generic logging of commands	normal
#11047	add ipython shell	normal
#11462	add/remove tool icons by drag/drop or context menu	normal
#11469	simplified workflows	normal
#11512	Assign different modes to mouse scroll wheel	normal
#11806	Clip all models with plane not parallel screen	normal
#12167	actions don't work on pseudobonds	normal
#13929	possibly change color-from-editor action behavior	normal
#14482	Improved task manager gui	normal
#1384	would like to control selection mode in selection command	low
#1777	Bond hiding does not work as expected	low
#1914	treatment of commands in script files	low
#2649	make colordefs permanent	low
#2732	select none	low
#3443	put chemical info as balloon help over non-standard residue selectors	low
#5220	RFE: add "reasonable" keyword to "bond"	low
#8864	rlabelopt	low
#10229	Generalize dialog with a "don't show again" checkbox	low	Release 1.8
#11032	Model Panel: Surface inspector: show Surface Pieces as aggregate opt	low
#11035	balloon help for model widgets	low
#11041	buttons under command line to control model display	low
#11043	close-command-line button	low
#11067	improve Select...Zone	low
#11068	label offset in selection inspector	low
#1413	RFE: swapaa could allow chi angles to be specified	lowest
#10950	'set' command for misc. stereo params	lowest
#10951	command to control 3D label font/size	lowest
#11078	sinusoidal interpolation for reset	lowest
#11096	base dialog 'keepShown' should be boolean	lowest
#11105	Model Panel: have "transform as" use model-selection widget	lowest
#11107	exclusive-or selection mode	lowest
#11122	bfactor (and whatnot) in selection inspector	lowest
#11127	atomspec balloon delay pref	lowest
#11128	main open panel as extension with icon	lowest
Component: Graphics (17 matches)
Ticket	Summary	Priority	Milestone
#9087	allow for thicker selection outline	normal
#9148	would like silhouettes on lines or dashed cylinders	normal	none
#9847	Better display of model fit in map with slab clipping	normal
#9879	RFE: labels automatically offset to front	normal
#10284	Add visual depiction of double bonds	normal
#10589	Use fixed 30 degree initial field of view	normal
#10742	Don't recompute ribbons when only color changes	normal
#10763	Add commands to set eye separation and screen width	normal
#11246	Vary ribbon detail based on curvature	normal
#11247	Ribbon graphics per-residue instancing	normal
#11280	Make shadows account for clip planes	normal
#11284	dashed sticks	normal
#11363	Make transparent objects cast shadows?	normal
#11440	ribbon color blending	normal
#11756	Fade silhouette edges with depth	normal
#16781	Enable vertex buffer objects with Intel graphics	normal
#8992	nicer-looking transparent atoms	low
Component: Higher-Order Structure (11 matches)
Ticket	Summary	Priority	Milestone
#9703	SAXS enhancements	normal
#9813	Multiscale model color and display style commands	normal
#9842	Abstract depiction for a membrane with transmembrane protein	normal
#9878	Make multiscale resolution equal map resolution	normal
#10051	Modernize VIPERdb image creation script	normal
#10063	Make sym command handle unit cell symmetry	normal
#10237	replace PQS fetch with PISA fetch	normal
#11673	Output all-by-all marker distances	normal
#11696	Better representation of infinite symmetries	normal
#11820	Show biological units smaller than asymmetric unit	normal
#14417	Chimera does not display alternate representations from RMF files	normal	Release 1.11
Component: Infrastructure (8 matches)
Ticket	Summary	Priority	Milestone
#7482	Edit Trac ticket comments	normal
#8078	Make Chimera daily build download filename include version number.	normal
#10083	MATLAB interface to Chimera	normal
#10740	History of all operations	normal
#11212	http proxy does not allow authentication	normal
#19600	Chimera end-of-life release	normal
#8122	Put daily builds on web even if some build machine hangs	low
#8455	Add AppleScript support	low
Component: Input/Output (58 matches)
Ticket	Summary	Priority	Milestone
#2958	allow sequential residue numbering on output	normal
#3427	RFE: add MDL MOL/SDF to Browser Config	normal
#5056	Ask for image file name after raytracing	normal
#5769	read .x3d	normal
#6066	Need option to only export shapes, colors, and relative transforms	normal
#6085	depth cueing effect not strong enough	normal
#6531	Can't stop povray	normal	none
#7061	Embedding 3d graphics in PDF documents	normal
#7129	would like a "no shadow" option for POV-ray output	normal	none
#8441	RFE: write PQR format	normal
#8508	Web access despite userid/password	normal
#9919	Make session forward compatibility work more often	normal
#10082	Markers make session files large	normal
#10113	update SEQRES in saved PDB	normal
#10117	Add DARC database to fetch by id	normal
#10924	have 'write' command allow multiple models	normal
#10968	'write' command: choose format based on suffix if 'format' omitted	normal
#10975	better site-wide PDB dir mechanism	normal
#11309	Add transparent background option to copy command	normal
#11570	Remove functions from Chimera sessions	normal
#11587	Box beam sculpture user interface	normal
#12237	Slow frame rate, space navigator	normal
#12315	Fetch from nearest database mirror	normal
#12663	ignore non-standard columns past coords in ATOM/HETATM	normal
#12832	RFE: make missing results from PDB2PQR more obvious	normal	Release 1.11
#444	icons instead of slashes	low
#3430	use Windows Internet Shortcuts	low
#4565	handle ~ expansion	low
#8003	Make "write" command accept multiple models	low
#8361	also export ribbons in .obj format	low
#8865	read mol2 files containing GAFF atom types	low
#9222	write PDBQT files	low
#10977	preserve open/save dialog size through close/open	low
#11040	option to change AMBER residue names to standard residue names before writing out	low
#11048	group File->Open types	low
#11056	combine write PDB/Mol2 dialogs	low
#11063	support bz2 compression	low
#11116	support SCOP sunid	low
#11225	Simplify image save dialog	low
#10978	open/save smooth scrolling	lowest
#10979	open/save "desktop" button	lowest
#10980	less horizontal scrolling for two-panel browser	lowest
#10981	Open/Save: document run() for modal dialogs	lowest
#10982	open/save: just one "all" if only one type filter	lowest
#10983	open/save: make dirFaves handle drive letters	lowest
#10984	open/save: run "no such path" modally on Windows	lowest
#10985	open/save: sort "ask file type" case independent	lowest
#11070	write PDBML	lowest
#11071	have neon handle all pseudobonds	lowest
#11074	omit unneeded TERs	lowest
#11082	use more info from Gaussian checkpoint file	lowest
#11099	warn when symmetry applies in LINK record	lowest
#11100	handle mixtures	lowest
#11101	deal with numeric insertion codes	lowest
#11108	if non-standard atom names detected, reassess previous atoms	lowest
#11119	"advanced options" for main File->Open	lowest
#11120	read/write GAMESS/Gaussian 98 z-matrix	lowest
#11126	PDB browser	lowest
Component: MD/Ensemble Analysis (41 matches)
Ticket	Summary	Priority	Milestone
#9455	store some info on a per-frame basis	normal
#10998	MD: graphing: # H-bonds	normal
#10999	MD: graphing: # energy	normal
#11000	MD: graphing: nearby ions/solvent	normal
#11001	MD: graphing: inter-helix angles	normal
#11002	MD: graphing: cavity volumes	normal
#11003	MD: graphing: user-defined properties	normal
#11004	MD: graphing: values from file	normal
#11005	MD: scatterplot of per-frame value pairs	normal
#11006	MD: histograms of graphed values	normal
#11007	MD: show multiple frames	normal
#11008	MD: trajectory smoothing	normal
#11009	MD: show ptraj's principal component analysis	normal
#11010	MD: depiction H-bond presence	normal
#11011	MD: allow .gro as substitute for .tpr	normal
#11012	MD: RMSD map: put clicked value in non-transient location	normal
#11016	MD: atom attr of match distance for frame pair	normal
#11112	MD: expose atom-type data	normal
#11460	MD Movie: "bounce" looping	normal
#13982	Ramachandran plotting of trajectories	normal
#2144	allow use of PDB instead of PSF	low
#3139	remember play direction so "un-pause" will work	low
#3442	better frame specification when saving PDB	low
#3454	color by displacement	low
#5179	allow automatic secondary structure updating	low
#8250	"max and match" of topology/coordinate formats	low
#10121	visualize periodic boundaries	low
#10122	duplicate periodic system	low	Release 2.0
#10414	per-residue RMSD compution	low
#10751	MD Movie: highlight cluster on RMSD map	low
#11013	MD: OKing cleared script == stop running script	low
#11014	MD: generate intermediates	low
#11015	MD: frame -> model	low
#11017	MD: hbonds for trajectory	low
#11019	MD: residue contact map	low
#11539	allow interactive clustering adjustment	low
#11018	MD: fast RMSD	lowest
#11020	MD: convert PDBio errors to user errors	lowest
#11021	MD: Ramachandran plots	lowest
#11022	MD: "rock" button	lowest
#11023	MD: enhance DCD reading for 64-bit CHARMm	lowest
Component: Movement (6 matches)
Ticket	Summary	Priority	Milestone
#9806	Want savepos/reset without changing camera view	normal
#10064	Undo relative motion keyboard shortcut	normal
#10798	Turn command on part of a molecule	normal
#12203	Precession axis with coordinate system specified gives weird motion	normal
#13858	Constrain rotation about screen axes	normal
#14028	Fix center of view rotation while rotating	normal
Component: Performance (5 matches)
Ticket	Summary	Priority	Milestone
#11255	C++ implementation of Match->Align	normal
#11385	Optimize opening molecules	normal
#11093	minimize calls to preferences.save()	lowest
#11106	convert Needleman-Wunsch to C++	lowest
#11124	optimize ChemGroup	lowest
Component: Platform (2 matches)
Ticket	Summary	Priority	Milestone
#11319	Chimera WebGL viewer	normal
#11581	Use full resolution on mac retina displays	normal
Component: Sequence (66 matches)
Ticket	Summary	Priority	Milestone
#9966	RFE: incorporate resulting alignment when blasting from MAV Tools	normal
#9975	Use BLAST to report all binding partners in PDB	normal
#10112	delete alignment columns	normal
#10839	MAV: start/end Region Browser columns	normal
#10862	MAV: compute % identity for active region	normal
#10863	MAV: gray out SS params if inapplicable	normal
#10864	MAV: allow "diffing" of node/seq against consensus/node/alignment	normal
#10865	MAV: helix/coil/etc support for headers	normal
#10866	MAV: manual creation/editing of headers	normal
#10869	MAV: rework dendrogram handling to allow node hiding	normal
#10870	MAV: handle seq add/delete when dendrogram present	normal
#10871	MAV: hide/show dendrogram nodes	normal
#10872	MAV: delete dendrogram node	normal
#10873	MAV: save dendrogram/node	normal
#10874	MAV: read dendrograms in NEXUS format	normal
#10875	MAV: consensus/conservation of sequence subsets	normal
#10876	MAV: depict region around dendrogram node sequences	normal
#10877	MAV: depict numeric dendrogram branch weights	normal
#10878	MAV: allow restriction of operations to dendrogram nodes	normal
#10879	MAV: all num seqs != num dendrogram leaves	normal
#10880	MAV: allow visual separation of dendrogram nodes	normal
#12388	allow conservation to be shown for sequence subsets	normal
#12810	RFE Blast Protein: choose "A" chains as best-scoring per PDB	normal
#12811	RFE Blast Protein: allow deleting or hiding specific results	normal
#13237	MAV: easier ensemble association	normal
#13239	improved header range mapping	normal
#9860	Show model sequences aligned	low
#10693	command version of Match->Align	low
#10867	MAV: support plugins for defining regions	low
#10883	MAV: allow all-by-all % identity to be formatted as a matrix	low
#10884	MAV: remove Assess Match	low
#10885	MAV: align struct seq based on distance from structures	low
#10886	MAV: command line capabilities	low
#10887	MAV: region "inspection"	low
#10888	MAV: finer-grained font control	low
#10889	MAV: optimize AL2CO	low
#10891	MAV: use label for single-chain structure in associations dialog	low
#10892	MAV: show alignment indels on structure	low
#10893	MAV: conservation by amino-acid category	low
#10894	MAV: interpret PHD/Psipred/profsec output	low
#10895	MAV: show auxiliary sequence info	low
#10896	MAV: inspector for file/sequence attrs	low
#11046	compose sequence aligns using MUSCLE or T-Coffee	low
#11064	additional nucleic acid ambiguity codes	low
#11065	support Gonnet250 similarity matrix	low
#12317	RFE: have MAV-Modeller interface handle multi-chain modeling	low
#12812	RFE Blast Protein: input option "from UniProt"	low
#12848	align unaligned sequences	low
#10060	note "reviewed" (Swiss-Prot) status of UniProt entries	lowest
#10901	MAV: update superposition during alignment edit	lowest
#10902	MAV: match ribbon/letter colors	lowest
#10903	MAV: associate multiple chains	lowest
#10904	MAV: change residues	lowest
#10905	MAV: GUI for residue-type (only) color scheme definition	lowest
#10907	MAV: show Stockholm GR markups next to marked up sequences	lowest
#10908	MAV: submit alignment to Consurf	lowest
#10909	MAV: more preferences	lowest
#10910	MAV: color conserved columns	lowest
#10911	MAV: column/row/sequence annotation editing	lowest
#10912	MAV: control of default region colors of pred/actual SS	lowest
#10913	MAV: add sample data	lowest
#10914	MAV: hide columns that don't have an uppercase character	lowest
#11091	swapaa doesn't change sequence panel	lowest
#11102	abort button for Match->Align	lowest
#11103	Match->Align: option to keep selected residues aligned	lowest
#11117	have Smith-Waterman return range of match	lowest
Component: Structure Analysis (43 matches)
Ticket	Summary	Priority	Milestone
#7813	FindHBond: all restriction to btw. 2 arbitrary groups of atoms	normal
#9456	thermal ellipsoids on a per-frame basis	normal
#9728	always report centroid in model coordinates	normal
#9849	Atom distance measurement mouse mode	normal
#10837	more compatibility for Axes/Planes/Centroids	normal
#10920	Metal Geom: bulk dump of ligand angles	normal
#10921	Metal Geom: add missing metal based on ligands	normal
#10925	make 'angle' command work with 3/4 centroids	normal
#10929	show additional axes in Axes tool	normal
#10930	integrate dipole-moment calculation	normal
#10931	Axes: helix fitting using fit to cylindrical surface	normal
#10940	command to save defattr file	normal
#10957	pseudobond panel button for writing out group	normal
#10959	Render by Attr: place middle histogram bar at zero if appropriate	normal
#10960	FindHBond: element-0 "atoms" handling	normal
#10963	allow clashes to reveal hidden structure	normal
#10973	command to report phi/psi/omega/chi angles	normal
#11059	contact maps	normal
#11333	Choose molecule regions for flexible fitting	normal
#11473	Excel export	normal
#12447	show normal to plane	normal
#12450	Make measure inertia depict inertia axes as marker model	normal
#12486	RFE: report full information of defined object in Reply Log	normal
#12866	RNA secondary structure annotations	normal
#14015	Chi symmetry	normal
#16820	Save log and input files for apbs	normal
#1766	Want to reset atom radii in render by attribute tool	low
#9792	FindHBond: report # of donors/acceptors	low
#10932	dist/~dist by ID	low
#11034	implement noeshow	low
#11037	show dipole moment	low
#11042	PBReader dialog: dashed lines	low
#11045	Define Attr: tell user when attr won't be shown	low
#11054	Render By Attr: complain if no residues worm-able	low
#11060	better support for attributes for bonds	low
#11061	undo atom radius-by-attr	low
#11076	open Attribute Calculator from Render By Attr	lowest
#11079	FindHbond: aromatic pi system as acceptor	lowest
#11080	FindHBond: check slop params	lowest
#11089	report radius of gyration	lowest
#11115	make chirality code more conformant to standard	lowest
#11118	find bond orders	lowest
#11125	order parameter analysis	lowest
Component: Structure Comparison (18 matches)
Ticket	Summary	Priority	Milestone
#7187	When aligning in a structure sequence, consider secondary structure markups of non-structure sequences	normal	none
#10134	Allow matchmaker command to move part of a molecule	normal
#10859	find best secondary-structure params for MatchMaker	normal
#10923	MatchMaker: animate matches	normal
#10958	"match pairings" group	normal
#10993	MatchMaker: use identical chains quickly	normal
#11330	Multi-molecule smooth morphs	normal
#11341	Calculate morphs faster	normal
#11364	Comparative Visualization web application	normal
#11472	align models via axes	normal
#11656	Allow extrapolation in morphing molecules	normal
#12977	RFE: purely structurally based superimposition	normal
#13348	multi-threaded MatchMaker	normal
#14317	Matchmaker: symmetric atom pruning	normal
#5351	RFE: allow specifying equivalences with input sequence alignment	low	none
#6051	Convenient default for chains to match	low
#11471	open to preserve zoom on CASP evaluation interface	low
#13340	RFE: un-tile improvement idea	low
Component: Structure Editing (46 matches)
Ticket	Summary	Priority	Milestone
#7341	have SMILES/PubChem fetching use Task Manager	normal
#7852	Want to halt energy minimization	normal
#9394	improve minimization speed (and/or warn user)	normal
#10043	Add RNA model building capabilities	normal
#10061	Allow split command to split a single chain into domains	normal
#10141	Minimize dock prep status messages uninformative	normal
#10850	"periodic table" of element buttons in Build Structure	normal
#10851	fragment editing	normal
#10852	valence warning during add bond	normal
#10853	icon for Build Structure	normal
#10854	use Engh/Huber bond length/angle values for peptides	normal
#10855	add/attach functional groups from a library	normal
#10856	Build Structure: allow higher valences for metals	normal
#10927	Build Structure: addaa functionality	normal
#10939	~addcharge command	normal
#10947	modify-atom command	normal
#10948	"place peptide" command	normal
#10965	AddCharge: allow estimated charges w/o confirmation	normal
#10976	add hydrogens to rotamers	normal
#10988	AddCharge: note in GUI that Gasteiger ignores formal charge	normal
#10995	AddH: restrict to selection	normal
#11168	convert more cofactor charge assignments to lookups	normal
#11351	Add Charge: treat NAG, MAN, etc. as standard	normal
#11466	interface to PyRosetta	normal
#11474	generate lipid bilayers	normal
#12873	Chimera-generated DNA differences from other programs	normal
#13595	RFE: Copy/Combine restricted to selection	normal
#13859	Allow easy copying of a selected part of a molecule	normal
#8857	allow dielectric constants other than 1	low
#9836	Combine more than 63 chains	low
#9875	Reduce protein to only C-alpha atoms	low
#10328	Make changechains command handle blank chain ids	low
#10949	command version of Dock Prep	low
#11033	AddCharge: GLYCAM params for carbohydrate residues	low
#11036	implement addna	low
#11038	AddH: give anilene 115 degree angle between bonds	low
#11044	Rotamers: dihedral driving	low
#11049	investigate molEdit.addDihedralAtom slowness	low
#11051	AddH: handle MSE automatically	low
#11052	atom name changing	low
#11055	AddH : cross check against FORMUL record	low
#12658	percentage protonation	low
#10997	AddH: multiple "unknowns" dialogs	lowest
#11069	command version of Build Structure	lowest
#11075	pKa-based protonation of phosphates	lowest
#11087	make "add bond" possible from context menu	lowest
Component: Surface (21 matches)
Ticket	Summary	Priority	Milestone
#7160	CMS Surface Code	normal
#8799	RFE: provide option to display solvent-accessible surface	normal
#9993	Spherical clipping of volumes	normal
#10009	Make Surface Color dialog update after scolor command used	normal
#10024	Inside and outside colors for surfaces	normal
#10025	Slab surface command	normal
#10378	Per-model surface cap color and style	normal
#10527	Allow hide dust and zone on same surface	normal
#11095	Remove molecule surface color source	normal
#11437	Single color caps with Surface Color dialog	normal
#11620	Measure buried volume	normal
#11664	Stops reporting surface values when transparency set	normal
#11712	Add singleComponent option to surface command	normal
#11763	Color surface patches with different methods	normal	Release 2.0
#11887	Show buried area	normal
#11950	Allow surface color to not color clipping caps	normal
#11956	Per-pixel surface coloring all white	normal
#12309	Add a copy surface command	normal
#12635	Make shape cylinder have sharp edge between tube and cap	normal
#9918	Remember surface all-component mode when calculation fails	low
#8456	need pre-clipped surfaces in X3D output	lowest
Component: Surface/Binding Analysis (9 matches)
Ticket	Summary	Priority	Milestone
#9116	Save CASTp info in sessions	normal
#10323	Coulomb grid calculation not allowed without surface	normal
#12004	RFE: support Hex format in ViewDock	normal
#14481	Upgrade APBS	normal	Release 1.11
#17183	Update DelPhiViewer to produce CUBE format	normal	Release 1.14
#5886	Fetch from CASTp hangs Chimera	low
#9245	RFE: calculate hydrophobic potential	low
#11066	interface finder	low
#12114	allow CASTp to match .poc/.mouth without using serial numbers	low
Component: Utilities (5 matches)
Ticket	Summary	Priority	Milestone
#8583	Color Key: allow option to space labels proportional to numeric values	normal
#10915	2D Labels: in commands, allow font size to be specified relative to window size	normal
#10916	2D Labels: show/edit IDs	normal
#10918	2D Labels: place images	normal
#10919	2D Labels: change justification	low
Component: Viewing Controls (5 matches)
Ticket	Summary	Priority	Milestone
#8657	focus in side view	normal	none
#10620	Display focal plane in side view in stereo mode	normal
#11951	Set zoom to specified Angstroms per pixel	normal
#12646	Add stereo command eye separation, focal plane distance options	normal
#2193	wall-eye eye separation problematic	low
Component: Volume Data (62 matches)
Ticket	Summary	Priority	Milestone
#9449	zone display does not work for solid volumes	normal
#9761	Specify cyclic and dihedral symmetry of helix maps	normal
#9763	Embed maps in session files	normal
#9764	Combine fit search with symmetry	normal
#9765	Read TOM motive list files, particle placement in tomograms	normal
#9767	Compute helix map symmetry parameters	normal
#9772	Allow symmetry products to describe N-start helices	normal
#9773	Show symmetry assigned to a map graphically	normal
#9808	Create a test suite volume close memory leak test	normal
#9822	Distance and angle measurement mouse mode	normal
#9823	Report EMfit fitting scores	normal
#9824	Make fitting maps keep specified atom pairs close	normal
#9825	Record placements of objects in maps	normal
#9826	Dialog interface for computing difference maps	normal
#9831	Standard deviation units for density maps	normal
#9832	Make one transparent layer the default for maps	normal
#9835	Specify target resolution for Gaussian smoothing	normal
#9838	Command to symmetrize a map	normal
#9839	Subtract molecule from map	normal
#9840	Assign resolution to map	normal
#9841	Mask map to eliminate dust (small connected blobs)	normal
#9844	More histograms in volume viewer	normal
#9848	Confirmation before closing a map	normal
#9850	Display map asymmetric unit	normal
#9851	Pad segmentation regions for masking	normal
#9853	Set map contour level to enclose specified molecular weight	normal
#9854	Remember preferred map contour levels	normal
#9855	Gaussian sharpening for maps	normal
#9912	Add copy map subregion command	normal
#9913	Report map positions at mouse	normal
#9994	Make fetch of EM maps work in background	normal
#10002	Show more volume dialog histograms	normal
#10048	RFE: command "sop clip" improvements	normal
#10263	Command to show oblique volume slices	normal
#10721	Make volume save command determine format from file suffix	normal
#11210	Color by local map resolution	normal
#11211	Show local correlation between molecule and map	normal
#11321	Display huge density map planes	normal
#11331	Segment symmetric maps	normal
#11504	Make morph map interpolate if grids not aligned	normal
#11600	Volume tracer doesn't move markers	normal
#11633	Volume transparency slider with color zone	normal
#11662	Add distance range option to mask command	normal
#11672	Place markers on map peaks	normal
#11807	Handle volume time series as a single map	normal
#11808	Map viewer tablet app	normal
#11856	Make measure correlation command take threshold level	normal
#11917	Flip map about x, y, or z axis	normal
#11975	Save segment map results in session files	normal
#12153	Make morph map morph colors.	normal
#12201	Show panel divisions in volume viewer dialog	normal
#12426	Package maps with session file	normal
#12644	Use EMDB suggested contour levels	normal
#12667	Make volumes use 64-bit offsets on 64-bit Windows	normal
#12903	Volume Eraser erase cube instead of sphere	normal	none
#13829	Allow fitting preserving symmetry axis	normal
#13882	Allow fit in map to use grid points of second map	normal
#13883	sop split makes it hard to reshow density map	normal
#13936	Add OME TIFF optical microscope map format	normal
#14258	Make molmap use b-factors	normal
#9950	Color MultiFit models to match original model colors	low
#11761	Solid benchmark incorrect scores	lowest

The following hand-maintained list of feature requests was discontinued in July 2011. It includes requests collected by Tom Goddard focussed on density maps, molecular assemblies, electron microscopy.

322. Compute helix map symmetry parameters. Several people at 3D EM GRC. July 1, 2011. #9767

321. Read IMAGIC map file format. Mario Dejung. July 1, 2011, #9766

320. Read TOM motive list files, particle placement in tomograms. John Briggs. July 1, 2011, #9765

319. Combine fit search with symmetry. John Briggs, others. July 1, 2011. #9764

318. Embed maps in session files. Several people at 3D EM GRC. July 1, 2011. #9763

317. Specify cyclic and dihedral symmetry of helix maps. Ed Egelman. July 1, 2011. #9761

316. Bending a filament map.
July 11, 2011
Andy Sen
Would like to bend a filament map so it follows a helical or sinusoidal path, e.g. to model a flagellum.

315. Spherical clipping.
July 5, 2011
Dan Cohen
Would like to clip a map to a sphere. Best if map was not masked, just display changed to show a spherical shell of a virus.

314. CIF crystal symmetry duplicate atoms.
June 23, 2011
Matthew Thompson
In CIF files representing small molecule crystals (e.g. ice) applying crystal symmetry can place copies of atoms right on top of themselves. Some web posts said this is normal and the duplicates should be eliminated. Chimera does not eliminate them. Perhaps it should. There are complexities in deciding where to place bonds then. Matthew Thompson sent an ice example which is particularly troublesome with half occupancies for 4 hydrogen positions around each oxygen.

313. Unify undo move.
June 8, 2011
Tom Goddard
There are three different motion histories that allow you to undo moves of atoms or models: Fit in Map, Movement Mouse Mode, and the Undo Move menu entry. All 3 histories are separate and none records everything. These should be unified into a single motion history.

312. Median filtering boundary values.
June 8, 2011
Danielle Jorgens, Tom Goddard
Median filtering puts zeros on the boundary of the volume box. Data from Danielle had 8-bit values ranging from 34-241. The median filtered version adds lots of mysterious 0 values outside the range of the original map values. That seems like an error since the median can't produce a value outside the original data range, unless you know about the weird zero filling on the boundary. Would be nice to improve the code so it gives the proper median boundary values. Will require 6 + 12 + 8 cases to handle grid points on faces, edges, and corners.

311. Smooth contour surfaces for masked volume data.
June 3, 2011
Ernesto Arias, Kelly Dryden
Is there anyway to smooth out the masked edge? I end up with chopped voxels (looks like stair-steps), rather than getting an interpolated smooth surface at the edge? When you mask volume data in Chimera using Volume Eraser or the mask command it sets the density values to zero outside the surface. In places where high density crosses the surface the masked result looks horrible -- volume contour surface is jagged with stair-steps following the pattern of the volume grid. I don't have any trick to make that surface look smooth. I have two ideas about how to approach the problem. One is to not have the density fall to zero immediately outside the surface. If it rolled off gradually the contour surface of the masked data would look better. I'm not optimistic that that will produce a good result. The second approach is to do something different from masking. Instead clip the volume surface with the sphere surface and cover the resulting holes with patches of the actual smooth sphere surface. I think this would look very nice and the patches of sphere could be a different coloring which would give a nice visual indication that you have cut through high density. I have not implemented either of these two ideas.

310. Make zones display in solid style rendering
June 3, 2011
Terry Lang, Ahmed Hassan
Would like volume zones to display the correct zone region when using solid style rendering. Currently it only works in surface/mesh rendering. In solid rendering it shows a rectangular subregion containing the actual zone around markers. Current way to work around the problem is to save the zoned map then reopen it. That sets values to zero outside the zone.

309. Make default fetch directory
May 25, 2011
Tom Goddard
Use ~/Downloads/chimera as a default fetch by id directory on all platforms. Create the chimera directory when it is needed if ~/Downloads exists. Does ~/Downloads exist on Windows and desktop Linux operating systems. Exists on Mac 10.x.

308. Allow choosing mirrors for Fetch by ID
May 20, 2011
Tom Goddard
Allow choosing mirror site for EMDB or PDB for fetch by id dialog. This is especially useful for EMDB where the downloaded maps can be large and bandwidth can be much higher using a local mirror.

307. Blend solid-style volume confocal data
May 4, 2011
Thomas Burgoyne
Recently I have started looking at 3D-confocal data and I discovered with a bit of work I can open the data using chimera. I open each colour channel as a separate image stack which works quite nicely. The only problem I encounter is when viewing the data using solid rendering only one channel is visible. Is there a way to view three image stacks at the same time using the solid rendering?

306. Read and write imgCIF density maps
May 4, 2011
Mattia Rocco
Is there any intention of implementing the uploading of imgCIF density maps files? Such files can be generated by RasMol starting from either atomic structures or low-resolution bead models (e.g. SAXS-derived models). Conversely, it would be nice if density maps could be generated within Chimera...

305. Allow changing chain identifiers
April 29, 2011
Francesco Burresi, dozens of other users
Would like to be able to change chain identifier of ligand so it differs from protein.

304. Brownian motion option for morph conformations
April 12, 2011
Greg Pintilie
Added Brownian motion option to morph command which jiggles atoms. Used in mmcpn animation gallery example made by Greg Pintilie.

303. Brownian motion option for fly and reset commands
April 12, 2011
Greg Pintilie
Add Brownian motion options to fly and reset commands for movie making. See the mmcpn animation gallery entry by Greg Pintilie for an example. Would take some amplitude parameter. May want to allow Brownian motion for just some models. Models are still treated as rigid. If multiple models jiggle, amplitude should relate to mass, or be independently specifiable for each model.

302. Extend map edges filling with zeros
April 4, 2011
Yocheved
I have a map with a box size 250,269,108. To run a map fitting script I need the map to have a cubic size. Using the volume viewer- Region min max step x - I was able to play with the box size the problem is I can't get the entire map into a cubic box (Z axis is to small). Is there a way to enlarge the box on the Z axis?

301. Renumber residues
March 22, 2011
Sumitro Harjanto
Is there a way to introduce a systematic offset to the residue numbering in a model? The numbering in my model is different from the convention. Eg. the methionine that's supposedly in position 5 is labeled as MET 4, alanine in position 6 as ALA 5, and so on. I can't do it manually cos there are many residues. Is there an easy way to resolve this other than using a script to automatically assign the labels? It'll be good if i can resolve this from the root , such that my atom specification is also consistent with the naming convention I use. :)

300. Select by attribute value command
March 8, 2011
John Beale
Make command equivalent for select by attribute tab of Render by Attribute dialog. Want this to select water molecules in a density map above specified density threshold for all frames of a molecular dynamics trajectory. This can be done currently with a atom specifier like "@/molDensity>3.5". A user might more easily find a command so probably still worth having that way of doing it too.

299. Values at atom positions command
March 8, 2011
John Beale
Make command equivalent for values at atom positions dialog. Want this to detect water molecules in a density map above specified density threshold for all frames of a molecular dynamics trajectory.

298. Color zone command
March 7, 2011
Huy Bui
I have a density map and 3 marker sets for coloring my density map. Is this possible to select the 3 marker sets and color my density map with a selected radius (Color Zone tool) by command line?

297. Labels for tiled models
February 23, 2011
Berhane Temelso, Javier Velazquez-Muriel
I often read in 1-30 hydrogen-bonded molecular clusters from XYZ files and tile them for analysis. It would be great to label each cluster/model with its chain ID or file name. Labeling them using the 2Dlabel command is inconvenient especially when I have a large number of models. Javi wants the same capability for tiled 2-d EM micrographs.

296. Add one extension in preferences
February 21, 2011
Zheng Yang
Would like to specify the directory for a single Chimera extension using Preferences / Tools, instead of the directory containing that extension since the containing directory may contain other stuff that should not be scanned as extensions.

295. Scripts menu
January 25, 2011
Elisabeth Ortega
Would like to be able to put Chimera scripts in a directory and have them appear in a top-level Chimera menu for easy execution. Elisabeth is working on adding this capability.

294. Replace PQS fetch with PISA fetch
January 19, 2011
Elaine Meng
PQS quaternary structure data base is no longer updated by EBI. Good replacement may be PISA which is maintained by the EBI.

293. Morph interpolation of EM data planes
January 19, 2011
Manfred Auer
Have serial section EM that shows objects (tubules) that are displaced from one plane to the next by distance comparable to object size. Want to be able to interpolate between planes to make a 3d visualization. Linear interpolation looks inadequate because too much is missing between planes. Morphing (e.g. as done by face morphing software) might provide sensible continuity between the planes. Would need to study many available 2-d image morphing packages to see if any could work on EM data (not human faces), and see how much manual specifying of matching control points is needed.

292. Reduce fit-in-map memory use
December 21, 2010
Tom Goddard, bug #8943
Reduce fit-in-map memory use by not allocating a full array of grid indices for a map being fit into another map when only grid indices above a threshold are being used. Currently the full grid index array is created then filtered. Could do this in one step with a simple C++ routine.

291. Thicker selection green outline
December 15, 2010
Daniel Gurnon
In preferences/background, the selection mode can be "fill" or "outline". Is it possible to add a line-width option for outline? I want to increase the thickness of a selection outline to make it easier for my students to see when I'm projecting an image, but I don't want to use the fill option and lose residue color information.

290. Make up-arrow/down-arrow keys work on multiscale models
December 10, 2010
Padmaja Natarajan, Tom Goddard
Would like the up arrow keys to act on selected multiscale model surface pieces like the Up button on the multiscale dialog, and the down arrow key should undo the selection promotion. The current arrow key code is explicitly coded for molecule atoms/residues/chains/molecules/all and may require substantial changes to handle multiscale hierarchies.

289. Position sphere key made by segment directioncolor command
December 8, 2010
Elaine Meng
Current positioning of sphere color key made by segment directioncolor command is pretty poor (at 0,0,0 in model coordinates), e.g. with EMDB 1283, far from segmentation surfaces. Could position according to displayed bounds instead.

288. Command to stitch marker chains
December 7, 2010
Gabe Lander
Could use a command to stitch marker chains to create a surface, as in Volume Tracer, used for masking and segmenting with a script.

287. Molecule subdivision makes zooming clunky
November 22, 2010
Mike Carnegie
Zooming in on a large molecule model causes freezes for seconds while a finer mesh is computed for the molecule display. These freezes greatly impair interactive viewing. It would probably be better in these large molecule situations if a finer mesh was not created. The improved zooming would be more valuable than the improved appearance for interactive analysis. Chimera bug #8991.

286. Atom spec balloons impair motion
November 22, 2010
Mike Carnegie
Rotating and zooming large volume surfaces is very clunky (2 second pauses) because atom spec balloons take seconds to compute. The atom spec balloon usually never appears so it is not clear what causes the long freezes. Would like some fix so that atom spec balloons do not impair performance rotating and zooming. Atom spec balloons can be turned off in preferences but they are quite useful for PDB models so simply disabling them is not a good solution. Chimera bug #8991.

285. Document volume and surface programming interfaces
November 12, 2010
Tom Goddard
Include documentation in the code of useful volume and surface Python and C++ functions and generate documentation from those code comments. This would speed up my new development that uses existing code, would encourage me to make more thoughtful interfaces to algorithms, and substantially encourage outside developers.

284. Surface rendering in Python
November 12, 2010
Tom Goddard
Port surface rendering code from C++ to Python using PyOpenGL. Most surface rendering code (excluding transparent rendering) does not require C++ for speed. Keep only the speed critical part in C++. This would enable easier development of new surface features such as clipped outline boxes, or separate inside/outside colors.

283. Solid volume rendering in Python
November 12, 2010
Tom Goddard
Port solid volume rendering code from C++ to Python using PyOpenGL. I don't think any part of the existing code requires C++ for speed. In Python it would be easier to add new capabilities like clipped outline boxes.

282. Volume slice tool
November 12, 2010
Tom Goddard
Allow displaying opaque gray-level volume slices on oblique slices when clipping a volume with near/far or per-model clip planes. The 3d volume and an clipped outline box of the volume would still be shown to provide context. Moving the slice would be done by moving the clip plane. Might also allow click and drag on the cut facet. Currently oblique slices can be shown with the volume dialog subregion selection panel. That method has several difficulties: not able to find it, moving slice is not intuitive, context provided by seeing volume behind slice and box outline not provided.

281. Clipped outline boxes
November 12, 2010
Tom Goddard
When a volume surface or solid model outline box is clipped with near/far or per-model clip planes show the outline at the clip plane. Currently the outline is simply clipped. Showing the outline would provide a good visual cue as to where the clipping is done, especially with solid volume rendering.

280. Crystal contacts between biological units
November 9, 2010
Padmaja Natarajan
Compute residues in one biological unit (PDB BIOMT records) that contact residues in other biological units in a crystal. Report residue pairs, contact distance, and buried surface area. This is related to the current crystal contacts Chimera tool but would use biological units instead of crystallographic asymmetric units, and also would report more detailed info. Would be used for Virus Particle Explorer database (VIPERdb).

279. Save multiscale per-vertex coloring in sessions
November 10, 2010
Stanislav Sosnovtsev
Would like per-vertex coloring of multiscale surfaces performed with the "msc" command to be saved in sessions. Wanted for ConSurf conservation coloring of virus capsid surface with solvent excluded surfaces.

278. Color zone with smooth edges
November 2, 2010
Xiaofeng
Would be nice if color zone produced colored regions with smooth edges. Currently the edges are jagged because the surface triangles that straddle the edge can only have coloring linearly interpolated from vertices. One solution would be to compute an equivalent surface where triangles that straddle two (or three) colors are split (and boundary vertices duplicated). They should be split at the point where the zone used in color zone ends. This surface recalculation is currently done by "measure contactarea" for patch display and produces beautiful results. Coloring a molecular surface by atom colors would also produce a much prettier result using this technique.

277. Surface mesh simplification for 3d printing
October 21, 2010
Joe DeRisi
Provide mesh simplification to reduce triangles in multiscale dialog virus surfaces (e.g. 3kz4, res 5A). The uPrint 3d plastic printer currently crashes on the large surface files (1 million triangles), apparently for lack of memory. Tried MeshLab using quadric decimation and 2x - 4x triangle reduction produced reasonable approximations though different in details.

276. Tiled display of EM 2d images
October 20, 2010
Javier Velazquez
Show tiled 2d images of particles from EM micrographs or class averages. Be able to apply common normalization (mean 0, sdev 1). This is done by xmipp_show program but that program is not widely used.

275. Add units option to SAXS dialog
October 19, 2010
Alex Shkumatov
Allow specifying nanometer or Angstrom units in SAXS dialog, also 2*pi factor. These apply to q value of experimental profile.

274. Side-Top-Front-Back View
September 29, 2010
YZ(originally from attendees at Pitt Chimera Workshop)
The main Chimera window could split into four, each of them shows the scene from side, top, front/back, prospective correspondingly.

273. Handle moved volume files gracefully
Bug #8781
September 14, 2010
Moving a volume file when it is open in Chimera causes errors when Chimera later needs to read more of the file. Currently it gives a traceback. It would be better to provide a user-friendly error message. Probably also need to assume the data is all zeros so that the code continues to function correctly when the data is gone.

272. Gaussian filter option to preserve value type
Monica Lin
August 6, 2010
Add option to gaussian filtering to preserve data type (e.g. unsigned 8-bit integer) instead of producing a 32-bit float values. The 32-bit values take 4 times more memory than 8-bit values that are typical in EM tomograms and fibsem and that size increase can greatly impair usability.

271. Report progress when cropping rotated volume
Monica Lin
July 29, 2010
Cropping a volume with a rotated selection box for a large tomogram may take minutes if the result causes thrashing, or is very large on a machine with very large memory. Would be nice to be able to see progress messages and cancel the operation. May be a rare situation. Happened with fibsem termite gut data.

270. File / Open dialog user directories
Tom Goddard
June 25, 2010
Want open and save dialogs to have a list of commonly used directories chosen by the user. Currently there is a list of the most recently used directories. That should also be available. I frequently find that my commonly used directories fall off the list of recently used ones. This problem has been dealt with by the native Mac file dialog and probably also the native Windows file dialog and those native dialogs should be used if possible.

269. Split map create smaller size volumes
Matt Dougherty
June 22, 2010
Have an option to the color zone dialog split map capability where the resulting volume copies are only as big as needed for the copied zone. This will save memory avoiding out-of-memory errors.

268. Supersampling volume data
Mario Borgnia
June 16, 2010
Make it easier to supersample volume data for example by a factor of 2 to reduce pixelation artifacts when rendering. Could be a vop command option.

267. POVray for solid style volume data
Mario Borgnia
June 16, 2010
Would like povray image saving for volumetric data. Apparently povray is able to render it (http://local.wasp.uwa.edu.au/~pbourke/miscellaneous/df3/).

266. Hide dust volume filter
Jason ODonnell
June 11, 2010
Would like to be able to zero density within small density blobs giving the same effect as the "hide dust" tool but using a density change instead of simply hiding parts of the contour surface. This could be an option to the vop comand. With it a morph between the original map and dust erased map would show the dust shrink and vanish -- an interesting way to animate hiding the dust.

265. Hide dust command
Matt Dougherty
June 10, 2010
Would like a command equivalent to the hide dust dialog. It should also be able to simply color the dust or add transparency. Could use this to fade the dust in an animation. For that it would be useful if there was a "frames" option to specify over how many frames to make the change over.

264. Cross-fade option to movie command
Matt Dougherty
June 10, 2010
Would like to have a movie command "fade" option that does a cross-fade between the preceding captured frame and the next captured frame. Might look like "movie fade frames 25". Would use this to animate hiding dust.

263. Session restore don't change window size
Tom Goddard
June 10, 2010
Want to be able to open session files without having the Chimera window resize. This is useful when giving a demonstration with a full screen Chimera window and showing several sessions. I think the best way to do this is to have a preference, "Session restore changes window size" defaulting to true. On the demonstration computer the preference could be set to false.

262. Command to set bond length
Le Monk
May 25, 2010
Would like command to set bond length. This capability is in the build structure dialog.

261. Motion blur image from recorded movie
Lila Rubenstein, Jie Fu
May 18, 2010
Would be neat of movie recording could optionally produce a motion blurred single image from start to end of the movie. It would be used with morph conformations to show a motion in a static image. It could have parameters indicate how bright the intermediate blur is relative to the start and end images. Might also have an option to dim the start state (or end state). This would be a pretty simple to implement accumulating the image from the captured images.

260. Make multiscale handle CA-only chains with ligands
Batsal Devkota
May 11, 2010
Want a more robust way to choose the contour level for making Multiscale surfaces. Bug report #8353 describes a case where a PDB file has CA-only protein chains combined with all-atom ligands. The Multiscale dialog thinks this is an all-atom model and uses an atom-density appropriate for an all atom model to make the surface depiction. The resulting surface is empty because of the low actual density.

259. Command to set transform matrix
Vijay Reddy
April 28, 2010
Would like to be able to specify a transformation matrix as a 3x4 matrix to apply to some specified models. Could conceivably add a rotation matrix option to the turn command. But it would complicate thet command syntax since it now requires axis and angle as fixed position (non-keyword) parameters. Might want to either set the transform or apply the transform to the existing orientation. Might want to apply it in local or global coordinates.

258. Project volume data to 2-d
Ryo
April 27, 2010
Want to project an 3-d volume data set to 2-d including projection along axes other than the data x, y or z axes. Could be added to the vop command and could use existing resampling capability to project along non-data axes.

257. Command to set view direction
Vijay Reddy
April 27, 2010
Would be useful to have a command to set the view direction along an axis specified with 3 coordinates in order to be able to look down the symmetry axis of a map or molecular assembly (e.g. pentamer of a virus).

256. Single click to show single volume
Mike Schmid
April 2, 2010
Want a single-click way to show a specific volume and hide all other volumes. How about right-click on volume dialog show map icon? How can switching between more than 3 maps be most easily handled?

255. Command to set surface cap color
Jean-Paul Armache
March 5, 2010
I would like to ask you whether there is a way to change the cap color not only from the Surface capping tool, but the command line as well and declare it maybe in a script (like for example coloring of the maps and models). Should have surface cap command to control whether caps shown/hidden, mesh/fill style, subdivision, offset. Best if these were settable on a per-surface basis (not possible in dialog). The same command might control general surface properties.

254. Group models
Jean-Paul Armache
March 3, 2010
I am often juggling between different sets that are to be turned on/off together. Is there a way of grouping maps/pdbs so that instead of turning 20 pdbs on, i could just click on a group to which they belong ? If there is something like that, could you point me to it ? And if not, would it be possible to have it in the Model Panel?

253. New command "active"
Tom Goddard
March 3, 2010
Create a new command "active" to specify which models are active (ie. movable). Currently this is done with the misleadingly named "select" command provided the model number argument isn't preceded with "#". If the argument does start with "#" then "select" behaves differently controlling selection instead of activation. This senseless and confusing select command was an attempt to preserve the historical "select" command for activating models. "select" for activating models should be deprecated and a new command "active" should do this job. This message points out contortions that are encountered without the "active" command.

252. Display principal axes for sets of atoms
Giuseppe Falini
February 12, 2010
I am using Chimera to create ellipsoids from specific sets of atoms. The ellipsoids are shown in the graphic window as a surface model and information about each ellipsoid are given in the reply log. In it the ellipsoid vectors are reported among others info. I wonder if you have a command to show vectors defining the ellipsoid instead of the surface model in the graphic window.

251. Background image/movie creation for databases
Tom Goddard
February 10, 2010
Here is an idea for producing images and movies in nogui mode in Chimera. My interest in this is because my San Diego visit tomorrow is to an NCRR center (NRAMM) that automates EM data collection and processing and they like to automatically make Chimera images and movies using this background pipeline. Of course, they can (and maybe do) use the Linux Headless Chimera version for this. But why not make it easier by not requiring a special Chimera and particular operating system? Could Mesa be included in the standard Linux Chimera and when the --nogui flag is used it could set LD_LIBRARY_PATH to link to Mesa instead of the system OpenGL to allow background image/movie creation without being logged into the console? If Mesa builds on Mac and Windows they could also do this too? Allowing public database sites to generate images and movies as a background console-less process without requiring a special Chimera that is now available on only one operating system might encourage that use. Although there are relatively few databases who might use that, the impact of having Chimera images on those sites may justify the effort. Currently the PDB, EMDB (EM Navigator Japan PDB), and NRAMM resource (San Diego) do database image generation with Chimera. Not sure if Andrej Sali uses it for ModBase -- that could be another customer.

250. Volume thresholding
Michael Zimmermann
February 2, 2010
Allow the vop command to set volume data values below a given threshold to a specified value. Also allow setting data values above a given threshold to a specified value.

249. Renumber residues
Jonathan Sheehan
January 28, 2010
Two of the most common tasks I need to do when constructing a model are: renaming the chains in the structure, and renumbering stretches of residues. I can imagine two menu items similar to "Actions->Atoms/Bonds->Delete" named "Set chain ID..." and "Renumber residues from..." that could operate on the current selection. I suspect these menu options (or something similar, maybe under "structure editing"?) would be helpful to many folks. It could be a lot faster / easier than generating the right awk line or venturing into Emacs' PDB-mode.

248. Rename chains
Jonathan Sheehan
January 28, 2010
Two of the most common tasks I need to do when constructing a model are: renaming the chains in the structure, and renumbering stretches of residues. I can imagine two menu items similar to "Actions->Atoms/Bonds->Delete" named "Set chain ID..." and "Renumber residues from..." that could operate on the current selection. I suspect these menu options (or something similar, maybe under "structure editing"?) would be helpful to many folks. It could be a lot faster / easier than generating the right awk line or venturing into Emacs' PDB-mode.

247. Circular ribbon dislay
Volodymyr Babin
January 28, 2010
I would like to visualize a circular molecule using ribbons. As far as I can tell, with the current code ribbons always have ends (cannot be closed).

246. Save SAXS profile results in a file
Tom Goddard
January 26, 2010
The SAXS profile calculation should provide the capability to save the FoXS output file to disk, especially when it was computed using a web service. This allows the user to analyze it outside Chimera.

245. Display SAXS fit chi value
Dina Schneidman
January 26, 2010
The SAXS profile plot should display the chi value for the fit to the experimental data. This found in the header of the output file.

244. Make "wait" command with no arguments work with volume planes
Bridget Carragher
January 23, 2010
The wait command with no arguments does not wait for the "volume planes" command. Also does not wait for the vop morph command. Also probably does not wait for surftransparency command with frames argument. Make "wait" with no frame count wait for all commands that take frame count arguments.

243. Show distances to nearby atoms
Miguel Ortiz Lombardia
January 20, 2010
Want to display distances graphically from selected atoms to all other atoms within a specified distance.

242. Silhouettes for dashed lines
Thomas Mitterfellner
December 22, 2009
Would like silhouette edges for bond wire display especially when using dashed lines. An alternative would be to support dashed stick bonds.

241. Thumbnail images within session files
Thomas Marlovits
December 22, 2009
Have sessions contain thumbnail images which can be viewed in Chimera file browser and ideally in Windows/Mac/Linux file browser too.

240. Distance measurement without graphical display
Bala Subramanian
December 22, 2009
Want to record distance between two atoms in every frame of an MD trajectory. "distance" command executed twice with same atoms gives an error. Requires also doing ~distance in per-frame script. Make the ~distance unnecessary. Add distance measurement to "measure" command.

239. Up-arrow custom atom groupings
Thomas Mitterfellner
December 22, 2009
Allow user to specify atom groups for extending selections with up-arrow key.

238. Hide selected pseudobonds with Actions / Atoms+Bonds / hide
Vijay Reddy
December 21, 2009
It is easy to select missing segment pseudobonds with the mouse (select one then press up-arrow key), but figuring out how to hide them is then difficult. Seems most obvious that menu entry Actions / Atoms+Bonds / hide should hide them but it does nothing currently.

237. Report center coordinates of molecule
Bala Subramanian
December 18, 2009
Make measure command able to report geometric or mass weighted center of specified atoms.

236. Improve programming examples
Will Moore
December 14, 2009
Note in programming examples whether you are intended to cut and paste code into the IDLE window or simply load a script. I don't know what was intended. Use full paths to files, or say that Chimera must be started in the directory containing the needed files, or explain how to use Chimera "cd" command to change to directory containing needed files. Say how to run Chimera from a terminal on Mac OS. Do the examples say to run Chimera from a command-line? Would be useful for issue 2 above. What will be done on Microsoft Windows? The ToolbarButton.py doesn't work unless the "import re" and "import chimera" are in the function body. This is because Chimera deletes all globals after loading a file. This has often been a headache for me and Chimera should not delete globals.

235. Move specific models using saved positions
Chris Arthur
November 23, 2009
Savepos / reset allows moving all models and the camera settings to saved views. For moving making it would be helpful to add options to reset to not restore the camera position (use the current camera view and move the models), and also to only move specified models (relative to unmoved ones).

234. Command to report volume mean, sd, rms
Terry Lang
November 23, 2009
Make the measure volumestats command report mean, standard deviation and rms for a volume.

233. Introduce Chimera global coordinate system
Tom Goddard
November 18, 2009
Add a transformation matrix that describes the position of a new "global" coordinate system in the view frame. This transform would change when all models are rotated. The current model transforms would not change in that case. Currently the "model with lowest id" defines a sort of defacto global coordinate system. New models are opened aligned with that coordinate system. This is very confusing when models are moved relative to one another and a newly opened model aligns with an unintended model. In the proposed system the model transforms would only be used for relative model motions. We would know which models have been moved relative to the global frame (non-identity model transform). I believe this would make much more sense to the user.

232. Show model coordinate axes
Damien Lariviere
November 14, 2009
Is is possible in Chimera to display a reference frame? if yes, can we display the default one of the software or the one of a 3D structure? Would be nice to display 3-axes perhaps in 3 colors as in VMD for any specified model or for all models in the common case where they all share the same coordinate system. Might also have option to center axes depiction at center or corner of model bounding box.

231. Stereo parameter controls
Matt Dougherty
November 16, 2009
I am finding that getting the optimal stereo view requires ongoing adjustment of the stereo parameters, particularly when multiple people are observing the structure simultaneously (e.g., depthQ stereo projector). Currently these numbers have to be typed in, requiring me to break my gaze, move a mouse, and type a number. Ideally it would good to have controls similar to binoculars, such that you maintain constant view and adjust by turning knobs. Getting hardware knobs may be impractical, but these improvements could help. 1) two small buttons (+/-) next to each stereo parameter. 2) commands that would do the same (small incremental changes). Then I could have my nostromo n52 USB game box dedicate the dual axis thumb button for stereo adjustment by issuing keyboard commands.

230. Matrices from file with Multiscale tool
Damien Lariviere
November 18, 2009
Allow the sym command to read symmetry matrices from a file. Also allow the command to make multiscale surfaces instead of copies of the molecule.

229. Video documentation
Phil Bourne, Jeff Blaney, advisory committee
November 13, 2009
Make more short video clips explaining Chimera features. The commercial software for making screen capture videos could make the process much easier than what Andrew did in 2008.

228. Caps for clipped VRML surfaces
Damien Lariviere
November 17, 2009
After exporting multiscale surface as vrml and opening vrml in Chimera cannot get caps when clipping.

227. Position scalebar text better
Tom Goddard
November 6, 2009
Make the scale bar text which says the length of the bar (e.g. 100 A) center on the bar and offset nicely maybe 1/4 font height spacing above bar.

226. Easier way to select "turns"
Haixin Sui
November 6, 2009
Would like an easy way to select turns, ie all protein residues that are not helix and not sheet. The menu entry Select / Structure / secondary structure / "turn" does not do this, instead selecting residues specified in PDB TURN records -- seems almost useless in practical work. Perhaps that menu entry can just select non-helix non-sheet residues. There is a long command to achieve this "sel protein & ~ helix & ~ strand" but few if any users will figure that out.

225. Reduce volume resample temporary memory use
Lori Nyland
October 28, 2009
Volume resampling on a new grid is making a temporary copy of the interpolated data values in floating point - 4 bytes per grid point. This unnecessary memory use reduces the speed of resampling and limits volume size for large maps where there is not enough physical memory.

224. Make unit cell work with CIF files
Thomas Mitterfellner
October 28, 2009
Use cell parameters and space group from CIF header as is currently done for PDB files using CRYST1 record.

223. Silhouette edges for surface mesh
Thomas Mitterfellner
October 27, 2009
Would like silhouette edges for surface mesh, specifically for crystal unit cell outline.

222. Allow structure minimization to calculate only with selected residues
Tom Goddard
October 13, 2009
Currently the structure minimization tool can hold fixed unselected atoms but it still uses those atoms in computing forces. This can be extremely slow for large molecules (1 step per second for 5000 atoms). For simple loop minimizations only a local set of residues need be considered making the calculation extremely fast. I've tried this by deleting all the atoms that aren't needed for the minimization, minimizing (100 steps per second), then copying coordinates back to the full structure -- quite tedious.

221. Make command to copy a molecule
Tom Goddard
October 13, 2009
Have the mcopy command without a second argument make a new copy of the specified molecule(s). It's a pain to have to save a molecule to a file and reload it to make a copy.

220. Calculate hydrodynamic radius for EM map
Sudheer Molugu
October 13, 2009
There's a definition on wikipedia. Hydrodynamic radius is related to diffusion in solvent and also optical properties. Could perhaps use uniform solid bounded by map contour surface.

219. Make one layer mesh hide far mesh
Elaine Meng
October 13, 2009
Currently the one transparent layer surface option on mesh display just hides the far mesh lines at points where they cross near mesh lines -- almost no effect. Would be much more useful if it hid the entire far mesh as if the foremost mesh was a filled surface. This sounds easy, a matter of writing the filled triangles to the OpenGL depth buffer, but I this will obscure front mesh lines in places because the triangle and edge depths are not identical. Not sure.

218. Show/hide buttons under command-line
Elaine Meng
October 12, 2009
Replace the "active" buttons under the command-line with "shown" buttons. Toggling whether models are shown or not is much more common then whether they are active (ie can be moved with mouse).

217. Move connected atoms mouse mode
Elaine Meng
October 12, 2009
Make movement mouse mode able to move the connected atoms under the mouse. There's currently a keyboard shortcut (sc) to extend a selection to connected atoms and then the existing move selected atoms could be used. But eliminating the selection step could be useful. Also keyboard shortcuts are little used and Chimera has no non-shortcut means of selecting connected atoms.

216. Allow mmaker command to work on domains
Tom Goddard
October 5, 2009
Want to be able to control which domains are aligned between two homologous proteins for measuring relative domain rotations. Could work by simply concatenating specified residues to form the sequence for each set of residues. A very common case would have the domain specified as a contiguous set of residues e.g. #0:25-182 matched to #1:30-190. Another case common case would have the domain in two contiguous residue ranges, say #0:25-121,237-294 matched to #1:30-115,318-370.

215. Make turn command able to move parts of molecules
Tom Goddard
October 5, 2009
Allow turn command to move parts of molecules, for instance moving one domain relative to another in a hinge motion for fitting.

214. Make last down-arrow clear selection
Cathy Lawson
October 2, 2009
More convenient than the many alternatives (ctrl-click background, ~sel, shortcut cs).

213. Add "undo move" button to fit map dialog
Cathy Lawson
October 2, 2009
Probably can be the same as Tools / Movement / Undo Move. If fit in map is changed to allow moving only selected coordinates, undo move will have to be more sophisticated, or less desirable -- show a message indicating that can't undo if only some atoms of molecule are moved.

212. Silhouette edges don't fade out in movies
Tom Goddard
October 1, 2009
It is useful to fade in and out surfaces in movies by varying their transparency with the surftransparency command (e.g. "surft 100 #3 25" change surface #3 to 100% transparent over 25 frames). When showing silhouette edges the edges don't fade with the surface, making for an unsatisfactory fade out. Could the edges be made to match the transparency of the surface? I think that is not possible with the current stencil buffer algorithm. Silhouette edges are very useful for giving depth to transparent surfaces, so it would be nice to be able to use them in movie fades.

211. Brightness glitches in movies
Tom Goddard
October 1, 2009
Turning on display of a model during a movie often will cause the clip planes to move to encompass the whole scene (clipping off), that in turn causes the depth cuing to change. It's no problem in interactive use, but makes an annoying brightness glitch in recorded movies. Is there a way to avoid that glitch other than turning off depth cuing? What's a good way to handle this when recording movies?

210. Show virus gray levels on spherical surface
Tim Baker
January 23, 2009
Want to be able to interactively adjust sphere radius while displaying virus map gray levels on sphere. Chimera can do this now by combining the Icosahedron tool and surface color tool but there are two problems: 1) too slow when showing full resolution data, and 2) many steps required to set up this mode. The first problem is partially alleviated by the per-pixel coloring option of the surface color tool which allows full resolution volume data display on a coarse triangulated surface. But that requires that the full volume data fit in an OpenGL 3d texture which limits this technique to small maps. Would be useful to have a special purpose tool to ease the setup of this useful viewing mode. Baker lab uses RobEM program developed at Purdue for this but it can only handle limited map sizes.

209. Measure surface area and volume for partially hidden surfaces
Greg Couch
September 28, 2009
Would like to be able to measure surface area and volume using only the displayed portion of a surface (with measure command or dialog). Currently it uses hidden parts of the surface. Want this for measuring volume in an ion channel.

208. Allow hiding molecular surface pieces
Natalie Bordag
September 22, 2009
Want to hide the outer connected piece of a molecular surface and leave showing only the pocket surface. Maybe the separate connected surface pieces could be individually selected and hidden. Can do this in a bad way with shortcuts Sc (split connected) and Ds (delete surface pieces) but it makes the Actions / Surface menu not work. The associations between atoms and surface vertices gets messed up. Having molecular surface pieces individually hidable will require changes to the current implementation where visibility of surface patches is stored with atoms.

207. Allow changing model id number after model is opened
Thomas Marlovits
September 22, 2009
Provides flexibility for grouping models. Provides a mechanism for moving models independently that were initially created with the same model id number.

206. Join unit cell half benzene rings
Mike Day
September 4, 2009
Crystals with asymmetric units containing half a benzene ring are not handled well by the unit cell tool. The half benzene rings can appear far outside the unit cell boundaries and half benzenes from different asymmetric units are not covalently joined. Mike provided two example files iat03.pdb, ta21.pdb.

205. Make unit cell dialog work with CIF files
Mike Day
September 1, 2009
CIF files contain explicit symmetry operators that could be used by the unit cell dialog.

204. Allow recording movie with frame size larger than screen
Anastasia Aksyuk
August 28, 2009
Add option to movie command to record frames at a specified frame size instead of using the current window size.

203. Make ac command for running keyboard shortcuts work in nogui mode
Davide Bau
August 27, 2009
Some keyboard shortcuts don't have command equivalents so it can be useful to run the shortcuts from scripts. Currently the "ac" command for running shortcuts requires the shortcut dialog to exist preventing use in nogui mode.

202. Make vop subtract command interpolate like vop add
Elaine Meng
August 12, 2009
Should have vop subtract use interpolation like vop add. Will still want to provide exact subtraction of identical grids without round-off errors caused by interpolation. Probably subtract should use the grid of the first map and not extend to cover the other maps by default. For grids that are not identical, the maps may often come from separate sources and a normalization will have to be done. Could have an option to scale second map so deviation from first map is minimum (within second map contour level?). Also may want an explicit second map scaling so several copies can be subtracted using the same normalization. Difference maps have rather different requirements and purposes then adding maps.

201. Compute x-ray maps from structure factors
Michael Day, Rakesh Joshi
August 11, 2009
Want to compute x-ray maps (primarily small molecules?) from structure factors, possibly using SHELX from Chimera. Structure factors might be in MTZ format. Maps computed with COOT and CCP4 often have alignment problems in Chimera.

200. Volume tracer smooth path command Implemented shape tube command August 5, 2009
Davide Baú
August 3, 2009
Add command to make volume tracer smooth paths (curve radius, band length and segment subdivision).

199. Scroll-wheel for flipping through volume planes
Tom Goddard
July 21, 2009
Be able to switch the mouse scroll-wheel behavior from zooming the view to flipping through volume planes.

198. volume command subregion options Implemented July 28, 2009
Tom Goddard
July 21, 2009
Replace volume and vop useSubregion and useStep options with subregion and step that can explicitly specify the subregion and step with parameters. For example, the default would be "subregion current" and "step 1". But other possibilities would be "subregion all", "subregion 100,100,100,120,120,120", "step 2", "step 2,2,1". Probably keep the old options for compatibility.

197. Make all volumes writable
Elaine Meng
July 17, 2009
Making all maps writable including those read from files will eliminate an arbitrary and confusing restriction. Files will not be updated if the data is modified in memory.

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. Implemented coordset April 27, 2009
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, James Conway
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 reports #7148, #7644.

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. Implemented July 29, 2009
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. Implemented July 14, 2009
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. Partially solved with tile command August 3, 2009
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. Implemented August 17, 2009
D Greening, Thomas Margraf, others
July 14, 2008
Want space navigator support on Linux. Thomas Margraf has contributed code to use the space navigator in Chimera on Linux. It utilize libspnav (source forge project) and swig which would need to be included in Chimera builds.

149. Place markers on surfaces. Implemented June 4, 2009
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 ac command 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. Implemented glossy lighting December 30, 2008
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. Implemented January 7, 2009
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. See 2008 and 2009 movie making tutorials
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. Implemented 2009 in Chimera 1.4
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 in GUI.
Steve Ludtke.
November 15, 2007
Want to set the same contour level for several volumes (single particle reconstructions). Told Steve about new volume command that 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. Implemented measure rotation command January 7, 2009
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, Huy Bui.
August 20, 2007
Want IMOD surfaces that have been recolored in Chimera saved in session files. Huy wants unmodified IMOD models saved in sessions.

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. Implemented Space Navigator shortcut nf February 2, 2008
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. Done May 13, 2008
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. Implemented June, 2009
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. Done Marc 11, 2009
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 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. Projecting volume data.
Jeff Triffo, Ana Luiza
April 12, 2007
Allow averaging together neighboring planes in em tomography when displaying a single slice to improve signal to noise. This can be faked by displaying multiple planes in solid style and using orthographic rendering to project the stack. Add a "project" operation to vop command that takes a projection axis and produces a 2-d map (z grid size is 1).

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. Done about once a year, May 2009
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. EMDB added 2009
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. Measure command does this (Jan 2009).

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, Xiaofeng
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. Added measure command January 2009
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. Mask command 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. Mask command 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. Fetch EMDB maps and fit PDBs March 11, 2009
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. Export OBJ included in File / Export Scene (2008).

10. Chimera web page for electron microscopy. Volume guide created 2007
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. Measure inertia command Implemented July 24, 2009.
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. Fetch download directory added March 10, 2009.
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.