Changes between Version 38 and Version 39 of requests


Ignore:
Timestamp:
Aug 4, 2009, 3:40:03 PM (17 years ago)
Author:
goddard
Comment:

--

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  • requests

    v38 v39  
    3131<p>
    3232198.
    33 <b>volume command subregion options</b><br>
     33<b>volume command subregion options</b>
     34<font color=green>Implemented July 28, 2009</font><br>
    3435Tom Goddard<br>
    3536July 21, 2009<br>
     
    4344<p>
    4445197.
    45 <b>Make all volume writable</b><br>
     46<b>Make all volumes writable</b><br>
    4647Elaine Meng<br>
    4748July 17, 2009<br>
     
    191192<p>
    192193182.
    193 <b>Chimera command for playing MD trajectories.</b><br>
     194<b>Chimera command for playing MD trajectories.</b>
     195<font color=green>Implemented coordset April 27, 2009</font><br>
    194196Bala Subramanian<br>
    195197April 16, 2009<br>
     
    358360166.
    359361<b>Set contour level for specified enclosed volume.</b><br>
    360 
    361362Andrej Sali, others<br>
    362363Feb 25, 2009<br>
     
    367368165.
    368369<b>Mouse mode to delete connected markers.</b><br>
    369 
    370370Juha Huiskonen<br>
    371371Feb 25, 2009<br>
     
    376376164.
    377377<b>Make fitting move additional models.</b><br>
    378 
    379378Keren Lasker<br>
    380379Feb 17, 2009<br>
     
    386385163.
    387386<b>Zone outside radius.</b><br>
    388 
    389387Jean-Paul Armache<br>
    390388Feb 10, 2009<br>
     
    395393162.
    396394<b>Difference map when fitting.</b><br>
    397 
    398395Paul Dreizen<br>
    399396Jan 6, 2009<br>
     
    410407<p>
    411408161.
    412 <b>Add two volumes.</b><br>
     409<b>Add two volumes.</b>
     410<font color=green>Implemented July 14, 2009</font><br>
    413411Martin Kampmann<br>
    414412Dec 9, 2008<br>
     
    430428<b>Handle volume series as a single data set.</b><br>
    431429Sebastian Haase<br>
    432 
    433430July 21, 2008<br>
    434431Would like volume series handled as a single data set instead of separate
     
    444441Ed Brignole, Elaine Meng<br>
    445442July 17, 2008<br>
    446 
    447443Origin keyword argument in shape command could take 3 comma-separated numbers
    448444or an atom spec.  For numbers, might have a coords keyword to specify a model
     
    478474<b>Volume origin in index units.</b>
    479475<font color=green>Implemented September 9, 2008</font><br>
    480 
    481476Haixin Sui<br>
    482477July 15, 2008<br>
     
    509504<b>Periodic covering map command.</b><br>
    510505Terry Lang<br>
    511 
    512506July 15, 2008<br>
    513507Make a command that creates a map covering a PDB model using a periodic
     
    519513<p>
    520514151.
    521 <b>Tile newly opened models.</b><br>
     515<b>Tile newly opened models.</b>
     516<font color=green>Partially solved with tile command August 3, 2009</font><br>
    522517Eduardo Sanz Garcia<br>
    523518July 3, 2008<br>
     
    538533<p>
    539534149.
    540 <b>Place markers on surfaces.</b><br>
     535<b>Place markers on surfaces.</b>
     536<font color=green>Implemented June 4, 2009</font><br>
    541537Daniel Hautzinger<br>
    542538July 11, 2008<br>
    543 
    544539Place markers on a surface.  Wanted for AFM data.  This case actually
    545540probably better handled by existing capability to place on data planes.
     
    561556147.
    562557<b>Calculate difference map.</b>
    563 
    564558<font color=green>Implemented June 18, 2008</font><br>
    565559Jean-Paul Armache<br>
     
    574568Pradeep Pallan<br>
    575569May 12, 2008<br>
    576 
    577570Want to show a circle to indicate size of a molecular structure.
    578571</p>
     
    591584144.
    592585<b>Report area/volume in volume dialog.</b><br>
    593 
    594586Ed Brignole<br>
    595587May 12, 2008<br>
     
    610602143.
    611603<b>Command for running keyboard shortcuts.</b>
    612 <font color=green>Implemented April 8, 2008</font><br>
     604<font color=green>Implemented ac command April 8, 2008</font><br>
    613605Jean-Didier Marechal.<br>
    614606March 27, 2008<br>
    615 
    616607Would like a command for running a keyboard shortcut.  Makes shortcut
    617608capabilities easily accessible from a script.  Could extend "ac" command.
     
    632623141.
    633624<b>Optimize volume grid spacing to best fit a molecule.</b><br>
    634 
    635625Stefan Backstrom.<br>
    636626March 26, 2008<br>
     
    664654<b>Add per-model clip command "frames" argument.</b><br>
    665655Eric Pettersen.<br>
    666 
    667656February 22, 2008<br>
    668657The mclip command could use a "frames" argument, for moving the plane
     
    693682
    694683<p>
    695 
    696684136.
    697685<b>Less sensitive solid volume brightness / transparency.</b>
     
    706694<p>
    707695135.
    708 <b>Angle dependent transparency.</b><br>
     696<b>Angle dependent transparency.</b>
     697<font color=green>Implemented glossy lighting December 30, 2008</font><br>
    709698Andrew Jewett.<br>
    710 
    711699February 14, 2008<br>
    712700Scale surface opacity for oblique viewing angles.
     
    739727<b>Make capping on by default for per-model clip planes.</b>
    740728<font color=green>Implemented November 4, 2008</font><br>
    741 
    742729Tom Goddard.<br>
    743730February 8, 2008<br>
     
    778765129.
    779766<b>Read brix maps as 8-bit values.</b><br>
    780 
    781767Thomas Becker.<br>
    782768February 4, 2008<br>
     
    815801<b>Place markers on any visible volume.</b><br>
    816802C Akey.<br>
    817 
    818803January 25, 2008<br>
    819804Make volume path tracer place markers on any visible volume instead of just
     
    831816
    832817<p>
    833 
    834818124.
    835819<b>Extend map using symmetry.</b><br>
     
    850834<b>Color using MolMol electrostatic potential.</b><br>
    851835Esther Bullitt.<br>
    852 
    853836January 16, 2008<br>
    854837Read MolMol electrostatic potential grid data for coloring molecular
     
    879862<p>
    880863120.
    881 <b>Area/volume command.</b><br>
    882 
     864<b>Area/volume command.</b>
     865<font color=green>Implemented January 7, 2009</font><br>
    883866Zhiya Sheng.<br>
    884867December 26, 2007<br>
     
    917900<b>Easy hiding of all but one volume.</b><br>
    918901Eduardo Sanz Garcia.<br>
    919 
    920902November 26, 2007<br>
    921903Might make right click on show/hide oval above histogram hide all other
     
    958940<b>Animation extracting octant from virus density.</b><br>
    959941Yen-Chywan Liaw.<br>
    960 
    961942November 15, 2007<br>
    962943Wants to be able to extract an octant from a virus map.  Both pieces
     
    967948<p>
    968949112.
    969 <b>Animation where ligand flies into bound state.</b><br>
     950<b>Animation where ligand flies into bound state.</b>
     951<font color=green>See 2008 and 2009 movie making <a href="http://www.cgl.ucsf.edu/chimera/tutorials/tutorials.html">tutorials</a></font><br>
    970952Yen-Chywan Liaw.<br>
    971953November 15, 2007<br>
     
    992974<b>Reverse order of colors in
    993975<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html">surface color</a> tool.</b>
    994 
    995976<font color=green>Implemented April 17, 2008.</font><br>
    996977Yen-Chywan Liaw.<br>
     
    1002983<p>
    1003984109.
    1004 <b>Make POVray appearance better match Chimera window.</b><br>
     985<b>Make POVray appearance better match Chimera window.</b>
     986<font color=green>Implemented 2009 in Chimera 1.4</font><br>
    1005987Ed Egelman, others.<br>
    1006988November 15, 2007<br>
    1007 
    1008989Raytraced transparent volume surface images with povray have very different
    1009990transparency and brightness than what is seen in the Chimera window.  Since
     
    1014995<p>
    1015996108.
    1016 <b>Set contour levels for multiple volumes at once.</b><br>
     997<b>Set contour levels for multiple volumes at once in GUI.</b><br>
    1017998Steve Ludtke.<br>
    1018999November 15, 2007<br>
    10191000Want to set the same contour level for several volumes (single particle
    1020 reconstructions).  Told Steve about new volume command tha can do this.
     1001reconstructions).  Told Steve about new volume command that can do this.
    10211002Would be nice to have a way to do this in graphical user interface.
    10221003</p>
     
    10251006107.
    10261007<b>Set morph map contour level to preserve enclosed volume.</b><br>
    1027 
    10281008Pawel Penzcek.<br>
    10291009November 15, 2007<br>
     
    10381018Sebastian Haase.<br>
    10391019November 15, 2007<br>
    1040 
    10411020The current Chimera priism file reader only handles ZWT order (Z = z planes,
    10421021W = wavelengths, T = times) and refuses to read other orders.  Sebastian
     
    10461025<p>
    10471026105.
    1048 <b>Command to print relative model orientation.</b><br>
     1027<b>Command to print relative model orientation.</b>
     1028<font color=green>Implemented measure rotation command January 7, 2009</font><br>
    10491029Duncan Sousa.<br>
    10501030November 13, 2007<br>
     
    10561036104.
    10571037<b>Cubic volume interpolation.</b><br>
    1058 
    10591038Terry Lang.<br>
    10601039October 23, 2007<br>
     
    10891068<b>IMOD session saving.</b><br>
    10901069Jeff Triffo.<br>
    1091 
    10921070August 20, 2007<br>
    10931071Want IMOD surfaces that have been recolored in Chimera saved in
     
    11191097<b>Contour surface, include box boundaries.</b>
    11201098<font color=green>Implemented October 9, 2007</font><br>
    1121 
    11221099Tom Goddard.<br>
    11231100July 3, 2007<br>
     
    11301107<p>
    1131110897.
    1132 <b>Volume fly-through controls.</b><br>
     1109<b>Volume fly-through controls.</b>
     1110<font color=green>Implemented Space Navigator shortcut nf February 2, 2008</font><br>
    11331111Manfred Auer.<br>
    11341112July 2, 2007<br>
     
    11491127<p>
    1150112895.
    1151 <b>Color IMOD surfaces with Actions/Color menu.</b><br>
    1152 
     1129<b>Color IMOD surfaces with Actions/Color menu.</b>
     1130<font color=green>Done May 13, 2008</font><br>
    11531131Jeff Triffo.<br>
    11541132June 28, 2007<br>
     
    1180115892.
    11811159<b>Make multiscale tool work when atoms deleted.</b>
    1182 
    11831160<font color=green>Implemented October 25, 2008.</font><br>
    11841161Andy LiWang.<br>
     
    11941171Jawahar Swaminathan (MSD).<br>
    11951172May 24, 2007<br>
    1196 
    11971173Want to save Chimera images in nogui mode (no Chimera window shown)
    11981174to make virus capsid images for Macromolecular Structure Database.
     
    12231199Duplicate) and using the region bounds panel to limit the part of the
    122412003-d data displayed.
    1225 
    12261201</p>
    12271202
     
    1241121688.
    12421217<b>Show map standard deviation.</b>
    1243 
    12441218<font color=green>Menu entry to print mean/SD values October 10, 2007</font><br>
    12451219Holland Cheng.<br>
     
    12561230Request at UC Davis bay area cryoEM meeting.<br>
    12571231May 5, 2007<br>
    1258 
    12591232Allow reading "raw" maps -- file containing 3-d array of numbers.
    12601233User will specify
     
    1273124685.
    12741247<b>Fetch PDB biounit files.</b><br>
    1275 
    12761248Tom Goddard<br>
    12771249April 23, 2007<br>
     
    12851257Tom Goddard<br>
    12861258April 20, 2007<br>
    1287 
    12881259Provide user interface to control thickness of silhouette edges.
    12891260Often want thicker edges.  Can achieve this now by a trick -- making the
     
    13201291J Struct Biol. 2006 Oct 24; [Epub ahead of print]
    13211292</ul>
    1322 
    13231293which projects such annotations for virus capsids onto a sphere.
    13241294Also would like to overlay
     
    13451315
    13461316<p>
    1347 
    1348131780.
    13491318<b>Trace protein backbone.</b><br>
     
    13641333Xiaoyun Chen<br>
    13651334April 12, 2007<br>
    1366 
    13671335Want separate graphics windows for three orthogonal views: xy, yz and xz.
    13681336</p>
     
    1381134977.
    13821350<b>Path tracer marker attributes.</b><br>
    1383 
    13841351Jeff Triffo<br>
    13851352April 12, 2007<br>
     
    13971364<p>
    1398136576.
    1399 <b>Fetch EMDB maps.</b><br>
     1366<b>Fetch EMDB maps.</b>
     1367<font color=green>Done Marc 11, 2009</font><br>
    14001368Cathy Lawson<br>
    14011369April 12, 2007<br>
     
    14091377<b>Fetch PQS biological assemblies.</b>
    14101378<font color=green>Implemented April 27, 2007</font><br>
    1411 
    14121379Miguel Ortiz Lombardia<br>
    14131380April 12, 2007<br>
     
    14171384<p>
    1418138574.
    1419 
    14201386<b>Volume rendering size limit.</b><br>
    14211387Tom Goddard<br>
     
    14311397Anindito Sen<br>
    14321398April 12, 2007<br>
    1433 
    14341399Make pick surface pieces surface coloring save in session files.
    14351400</p>
     
    1451141671.
    14521417<b>Reoriented density maps.</b>
    1453 
    14541418<font color=green>Done for MRC and HDF formats September 4, 2007</font><br>
    14551419Tom Goddard<br>
     
    14641428<font color=green>Done with HDF, netcdf deprecated September 11, 2007</font><br>
    14651429Matt Baker<br>
    1466 
    14671430April 12, 2007<br>
    14681431Make netcdf writer automatically save subsampled versions of map in file down
     
    1500146367.
    15011464<b>Setting figure magnification.</b><br>
    1502 
    15031465Christopher Akey<br>
    15041466April 12, 2007<br>
     
    1511147366.
    15121474<b>Save BRIX format.</b>
    1513 <font color=green>Added prototype BRIX writer October 19, 2007</font><br>
     1475<font color=green>Added BRIX writer October 19, 2007</font><br>
    15141476Christopher Akey<br>
    15151477April 12, 2007<br>
    1516 
    15171478Write maps in BRIX format.  This is for interoperation with O for building
    15181479models in EM maps.
     
    15301491
    15311492<p>
    1532 
    1533149364.
    15341494<b>Save more EM map file formats.</b>
     
    15431503Tom Goddard<br>
    15441504April 12, 2007<br>
    1545 
    15461505Make 3-d arrows at morph map surface points of maximum change.
    15471506Implementation: Look at
     
    15611520
    15621521<p>
    1563 
    1564152261.
    15651523<b>Benchmark scores.</b>
     
    15771535<b>Color zone slider range.</b>
    15781536<font color=green>Implemented October 3, 2007.</font><br>
    1579 
    15801537Jeff Triffo<br>
    15811538April 12, 2007<br>
     
    16001557April 12, 2007<br>
    16011558Allow averaging together neighboring planes in em tomography when displaying
    1602 a single slice to improve signal to noise.
     1559a single slice to improve signal to noise.  This can be faked by displaying multiple
     1560planes in solid style and using orthographic rendering to project the stack.
    16031561</p>
    16041562
     
    16071565<b>Slicing EM maps.</b>
    16081566<font color=green>Resample volume added September 4, 2007</font><br>
    1609 
    16101567Jeff Triffo<br>
    16111568April 12, 2007<br>
     
    16211578Jeff Triffo<br>
    16221579April 12, 2007<br>
    1623 
    16241580Make volume zones work in solid display mode.
    16251581</p>
     
    1639159554.
    16401596<b>Volume rendering memory use.</b>
    1641 
    16421597<font color=green>Implemented September 6, 2008.</font><br>
    16431598Tom Goddard<br>
     
    16531608Jeff Triffo<br>
    16541609April 12, 2007<br>
    1655 
    16561610Make buttons and sliders to control perpendicular axis and translation of
    16571611per-model clip planes for volume data.
     
    16601614<p>
    1661161552.
    1662 <b>Update graphics driver bugs web page.</b><br>
     1616<b>Update graphics driver bugs web page.</b>
     1617<font color=green>Done about once a year, May 2009</font><br>
    16631618Tom Goddard<br>
    16641619April 12, 2007<br>
     
    1670162551.
    16711626<b>Crystal contacting chains.</b>
    1672 
    16731627<font color=green>Partially done October 10, 2007
    16741628(<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/crystalcontacts/crystalcontacts.html">crystal contacts</a> tool).</font><br>
     
    16851639<b>Atomic force microscope file reader.</b><br>
    16861640Alberto Roca<br>
    1687 
    16881641April 12, 2007<br>
    16891642Put nanoscope AFM tools on experimental features page.  Will need
     
    16931646<p>
    1694164749.
    1695 <b>Unit cell outline box.</b><br>
     1648<b>Unit cell outline box.</b>
    16961649<font color=green>Meshmol command can serve October 10, 2007</font><br>
    16971650Sabuj Pattanayek<br>
     
    1718167147.
    17191672<b>Volume subsample voxel origin.</b><br>
    1720 
    17211673Tom Goddard<br>
    17221674April 12, 2007<br>
     
    17341686Basal Devkota<br>
    17351687April 12, 2007<br>
    1736 
    17371688Allow two or more volume viewer dialogs for adjusting multiple maps easily.
    17381689</p>
     
    1749170044.
    17501701<b>Better multiscale surface quality.</b><br>
    1751 
    17521702Tom Goddard<br>
    17531703April 12, 2007<br>
     
    17631713Irina Serysheva<br>
    17641714April 12, 2007<br>
    1765 
    17661715Make volume subsampling not allocate unsubsampled array when reading from
    17671716file.  Limits reading of large data sets.
     
    17701719<p>
    1771172042.
    1772 <b>Collaboration descriptions.</b><br>
     1721<b>Collaboration descriptions.</b>
     1722<font color=green>EMDB added 2009</font><br>
    17731723Tom Goddard<br>
    17741724April 12, 2007<br>
     
    1779172941.
    17801730<b>Measure enclosed volume.</b>
    1781 
    17821731<font color=green>Added keyboard shortcuts mv and ma September 29, 2006</font><br>
    17831732Tom Goddard<br>
    17841733April 12, 2007<br>
    17851734Add option to measure volume/area to only measure selected surfaces.
     1735Measure command does this (Jan 2009).
    17861736</p>
    17871737
     
    17911741<font color=green>Added December 5, 2008</font><br>
    17921742Tom Goddard<br>
    1793 
    17941743April 12, 2007<br>
    17951744Add session saving to icosahedron tool.
     
    1817176637.
    18181767<b>Color zone with multiple radii.</b><br>
    1819 
    18201768Hernando Sosa<br>
    18211769April 12, 2007<br>
     
    18301778Elaine Meng<br>
    18311779April 12, 2007<br>
    1832 
    18331780Add split molecule command to Chimera distribution.  Makes each chain a
    18341781separate molecule.  Currently on experimental features web page.
     
    18591806<b>Surface coloring key.</b>
    18601807<font color=green>Implemented July 15, 2008.</font><br>
    1861 
    18621808Alexander Rusnak<br>
    18631809April 12, 2007<br>
     
    18711817Tom Goddard<br>
    18721818April 12, 2007<br>
    1873 
    18741819Investigate usability of Movie Recorder output formats on all common platforms
    18751820Windows, Mac, Linux.  See which work on stock operating system installations,
     
    1890183530.
    18911836<b>Volume commands for movies.</b><br>
    1892 
    18931837Frank Albers, Jeff Triffo<br>
    18941838April 12, 2007<br>
     
    19171861Haixin Sui<br>
    19181862April 12, 2007<br>
    1919 
    19201863Masking density to cylinders, masking with an external mask file.
    19211864Used for cylindrical virus particles.
     
    19321875<p>
    1933187626.
    1934 <b>Buried surface area.</b><br>
    1935 
     1877<b>Buried surface area.</b>
     1878<font color=green>Added measure command January 2009</font><br>
    19361879Tom Goddard<br>
    19371880April 12, 2007<br>
     
    1965190823.
    19661909<b>MSMS surface calculation with stand-alone program.</b>
    1967 
    19681910<font color=green>Implemented March 18, 2008.</font><br>
    19691911Tom Goddard<br>
     
    19791921<font color=green>Implemented January 8, 2008.</font><br>
    19801922Tom Goddard<br>
    1981 
    19821923April 12, 2007<br>
    19831924Make attribute inspector for surface models (volume, multiscale, ...)
     
    19971938
    19981939<p>
    1999 
    2000194020.
    20011941<b>Distribute Python modules separate from Chimera.</b><br>
     
    20111951Tom Goddard<br>
    20121952April 12, 2007<br>
    2013 
    20141953Make tools for slicing volume along a plane and enable moving of resulting
    20151954two pieces.  Might move them apart some as soon as sliced.  Make them
     
    2022196118.
    20231962<b>Mask map to icosahedron.</b>
    2024 <font color=green>Prototype surface masking October 17, 2007</font><br>
     1963<font color=green>Mask command October 17, 2007</font><br>
    20251964Wen Jiang, Gabe Lander<br>
    20261965April 12, 2007<br>
     
    2032197117.
    20331972<b>Masking within any surface.</b>
    2034 <font color=green>Prototype surface masking October 17, 2007</font><br>
     1973<font color=green>Mask command October 17, 2007</font><br>
    20351974Tom Goddard<br>
    20361975April 12, 2007<br>
     
    20431982<b>Volume solid rendering improvements.</b>
    20441983<font color=green>New transparency blending August 2, 2007</font><br>
    2045 
    20461984Sebastian Haase<br>
    20471985April 12, 2007<br>
     
    20722010<p>
    2073201113.
    2074 <b>EMDB / PDB fitting.</b><br>
    2075 
     2012<b>EMDB / PDB fitting.</b>
     2013<font color=green>Fetch EMDB maps and fit PDBs March 11, 2009</font><br>
    20762014Richard Newman, Cathy Lawson<br>
    20772015April 12, 2007<br>
     
    20972035April 12, 2007<br>
    20982036Add to experimental features page: volume statistics, export obj, and
    2099 nanoscope file reader.
     2037nanoscope file reader.  Export OBJ included in File / Export Scene (2008).
    21002038</p>
    21012039
    21022040<p>
    2103204110.
    2104 <b>Chimera web page for electron microscopy.</b><br>
    2105 
     2042<b>Chimera web page for electron microscopy.</b>
     2043<font color=green><a href="http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html">Volume guide</a> created 2007</font><br>
    21062044Tom Goddard<br>
    21072045April 12, 2007<br>
     
    21322070<b>Surface smoothing.</b>
    21332071<font color=green>Fixed by using gradient normals, October 6, 2007</font><br>
    2134 
    21352072Tom Goddard, Steve Ludtke<br>
    21362073April 12, 2007<br>
     
    21642101<p>
    216521024.
    2166 <b>Ellipsoid molecule display.</b><br>
    2167 
     2103<b>Ellipsoid molecule display.</b>
     2104<font color=green>Measure inertia command Implemented July 24, 2009.</font><br>
    21682105Tom Goddard<br>
    21692106April 12, 2007<br>
     
    21762113<p>
    217721143.
    2178 <b>Fetch by ID save button.</b><br>
     2115<b>Fetch by ID save button.</b>
     2116<font color=green>Fetch download directory added March 10, 2009.</font><br>
    21792117Tom Goddard<br>
    21802118April 12, 2007<br>
     
    219621341.
    21972135<b>Fetch EDS maps.</b>
    2198 
    21992136<font color=green>Implemented April 27, 2007</font><br>
    22002137Tom Goddard, forgot user<br>