Changes between Version 126 and Version 127 of requests


Ignore:
Timestamp:
Dec 15, 2010, 1:15:33 PM (15 years ago)
Author:
pett
Comment:

use strikeout text to emphasize completed rerquests

Legend:

Unmodified
Added
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  • requests

    v126 v127  
    10401040<p>
    10411041200.
    1042 <b>Volume tracer smooth path command</b>
     1042<strike><b>Volume tracer smooth path command</b></strike>
    10431043<font color=green>Implemented shape tube command August 5, 2009</font><br>
    10441044Davide Baú<br>
     
    10581058<p>
    10591059198.
    1060 <b>volume command subregion options</b>
     1060<strike><b>volume command subregion options</b></strike>
    10611061<font color=green>Implemented July 28, 2009</font><br>
    10621062Tom Goddard<br>
     
    12071207<p>
    12081208183.
    1209 <b>Command ` to focus next window on Mac.</b>
     1209<strike><b>Command ` to focus next window on Mac.</b></strike>
    12101210<font color=green>Implemented for Aqua April 24, 2009</font><br>
    12111211Chuck Sindelar<br>
     
    12191219<p>
    12201220182.
    1221 <b>Chimera command for playing MD trajectories.</b>
     1221<strike><b>Chimera command for playing MD trajectories.</b></strike>
    12221222<font color=green>Implemented coordset April 27, 2009</font><br>
    12231223Bala Subramanian<br>
     
    13281328<p>
    13291329172.
    1330 <b>Allow using markers without graphical user interface.</b>
     1330<strike><b>Allow using markers without graphical user interface.</b></strike>
    13311331<font color=green>Implemented July 29, 2009</font><br>
    13321332Daniel Russel<br>
     
    14341434<p>
    14351435161.
    1436 <b>Add two volumes.</b>
     1436<strike><b>Add two volumes.</b></strike>
    14371437<font color=green>Implemented July 14, 2009</font><br>
    14381438Martin Kampmann<br>
     
    14631463<p>
    14641464158.
    1465 <b>Add origin parameter to
    1466 <a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html">shape</a> command.</b>
     1465<strike><b>Add origin parameter to
     1466<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html">shape</a> command.</b></strike>
    14671467<font color=green>Implemented October 17, 2008</font><br>
    14681468Ed Brignole, Elaine Meng<br>
     
    14751475<p>
    14761476157.
    1477 <b><a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html">Turn</a>
    1478 command center of rotation argument.</b>
     1477<strike><b><a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html">Turn</a>
     1478command center of rotation argument.</b></strike>
    14791479<font color=green>Implemented October 17, 2008</font><br>
    14801480Haixin Sui<br>
     
    14991499<p>
    15001500155.
    1501 <b>Volume origin in index units.</b>
     1501<strike><b>Volume origin in index units.</b></strike>
    15021502<font color=green>Implemented September 9, 2008</font><br>
    15031503Haixin Sui<br>
     
    15401540<p>
    15411541151.
    1542 <b>Tile newly opened models.</b>
     1542<strike><b>Tile newly opened models.</b></strike>
    15431543<font color=green>Partially solved with tile command August 3, 2009</font><br>
    15441544Eduardo Sanz Garcia<br>
     
    15511551<p>
    15521552150.
    1553 <b>Space Navigator on Linux.</b>
     1553<strike><b>Space Navigator on Linux.</b></strike>
    15541554<font color=green>Implemented August 17, 2009</font><br>
    15551555D Greening, Thomas Margraf, others<br>
     
    15621562<p>
    15631563149.
    1564 <b>Place markers on surfaces.</b>
     1564<strike><b>Place markers on surfaces.</b></strike>
    15651565<font color=green>Implemented June 4, 2009</font><br>
    15661566Daniel Hautzinger<br>
     
    15841584<p>
    15851585147.
    1586 <b>Calculate difference map.</b>
     1586<strike><b>Calculate difference map.</b></strike>
    15871587<font color=green>Implemented June 18, 2008</font><br>
    15881588Jean-Paul Armache<br>
     
    16301630<p>
    16311631143.
    1632 <b>Command for running keyboard shortcuts.</b>
     1632<strike><b>Command for running keyboard shortcuts.</b></strike>
    16331633<font color=green>Implemented ac command April 8, 2008</font><br>
    16341634Jean-Didier Marechal.<br>
     
    17121712<p>
    17131713136.
    1714 <b>Less sensitive solid volume brightness / transparency.</b>
     1714<strike><b>Less sensitive solid volume brightness / transparency.</b></strike>
    17151715<font color=green>Implemented February 15, 2008</font><br>
    17161716Jeff Triffo.<br>
     
    17231723<p>
    17241724135.
    1725 <b>Angle dependent transparency.</b>
     1725<strike><b>Angle dependent transparency.</b></strike>
    17261726<font color=green>Implemented glossy lighting December 30, 2008</font><br>
    17271727Andrew Jewett.<br>
     
    17541754<p>
    17551755132.
    1756 <b>Make capping on by default for per-model clip planes.</b>
     1756<strike><b>Make capping on by default for per-model clip planes.</b></strike>
    17571757<font color=green>Implemented November 4, 2008</font><br>
    17581758Tom Goddard.<br>
     
    17791779<p>
    17801780130.
    1781 <b>Make crytal map and PDB model coincide.</b>
     1781<strike><b>Make crytal map and PDB model coincide.</b></strike>
    17821782<font color=green>Implemented Nov 20, 2007. Keyboard shortcut "bv" creates covering map.</font><br>
    17831783Trevor Sewell, Terry Lang.<br>
     
    18711871<p>
    18721872122.
    1873 <b>Multi-page TIFF image file reader.</b>
     1873<strike><b>Multi-page TIFF image file reader.</b></strike>
    18741874<font color=green>Implemented January 22, 2008</font><br><br>
    18751875Sebastian Haase.<br>
     
    18811881<p>
    18821882121.
    1883 <b>Correlation for fitting model in map.</b>
     1883<strike><b>Correlation for fitting model in map.</b></strike>
    18841884<font color=green>Implemented February 21, 2008</font><br>
    18851885C Akey.<br>
     
    18911891<p>
    18921892120.
    1893 <b>Area/volume command.</b>
     1893<strike><b>Area/volume command.</b></strike>
    18941894<font color=green>Implemented January 7, 2009</font><br>
    18951895Zhiya Sheng.<br>
     
    19081908<p>
    19091909118.
    1910 <b>Icoshedron mesh command.</b>
     1910<strike><b>Icoshedron mesh command.</b></strike>
    19111911<font color=green>Implemented January 24, 2008
    19121912(<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html">shape</a> command).</font><br>
     
    19771977<p>
    19781978112.
    1979 <b>Animation where ligand flies into bound state.</b>
     1979<strike><b>Animation where ligand flies into bound state.</b></strike>
    19801980<font color=green>See 2008 and 2009 movie making <a href="http://www.cgl.ucsf.edu/chimera/tutorials/tutorials.html">tutorials</a></font><br>
    19811981Yen-Chywan Liaw.<br>
     
    20012001<p>
    20022002110.
    2003 <b>Reverse order of colors in
    2004 <a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html">surface color</a> tool.</b>
     2003<strike><b>Reverse order of colors in
     2004<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html">surface color</a> tool.</b></strike>
    20052005<font color=green>Implemented April 17, 2008.</font><br>
    20062006Yen-Chywan Liaw.<br>
     
    20122012<p>
    20132013109.
    2014 <b>Make POVray appearance better match Chimera window.</b>
     2014<strike><b>Make POVray appearance better match Chimera window.</b></strike>
    20152015<font color=green>Implemented 2009 in Chimera 1.4</font><br>
    20162016Ed Egelman, others.<br>
     
    20432043<p>
    20442044106.
    2045 <b>Read PRIISM format volume files with WZT disk layout.</b>
     2045<strike><b>Read PRIISM format volume files with WZT disk layout.</b></strike>
    20462046<font color=green>Implemented June 3, 2008.</font><br>
    20472047Sebastian Haase.<br>
     
    20542054<p>
    20552055105.
    2056 <b>Command to print relative model orientation.</b>
     2056<strike><b>Command to print relative model orientation.</b></strike>
    20572057<font color=green>Implemented measure rotation command January 7, 2009</font><br>
    20582058Duncan Sousa.<br>
     
    21132113
    2114211499.
    2115 <b>Nintendo Wii controller for volume fly-through.</b>
     2115<strike><b>Nintendo Wii controller for volume fly-through.</b></strike>
    21162116<font color=green>Tested with DarwiinRemote September 27, 2007</font><br>
    21172117Dan Greenblatt.<br>
     
    21242124<p>
    2125212598.
    2126 <b>Contour surface, include box boundaries.</b>
     2126<strike><b>Contour surface, include box boundaries.</b></strike>
    21272127<font color=green>Implemented October 9, 2007</font><br>
    21282128Tom Goddard.<br>
     
    21362136<p>
    2137213797.
    2138 <b>Volume fly-through controls.</b>
     2138<strike><b>Volume fly-through controls.</b></strike>
    21392139<font color=green>Implemented Space Navigator shortcut nf February 2, 2008</font><br>
    21402140Manfred Auer.<br>
     
    21462146<p>
    2147214796.
    2148 <b>Better error message when volume data too large.</b>
     2148<strike><b>Better error message when volume data too large.</b></strike>
    21492149<font color=green>Done August 23, 2007</font><br>
    21502150Irina Serysheva, Matt Dougherty.<br>
     
    21562156<p>
    2157215795.
    2158 <b>Color IMOD surfaces with Actions/Color menu.</b>
     2158<strike><b>Color IMOD surfaces with Actions/Color menu.</b></strike>
    21592159<font color=green>Done May 13, 2008</font><br>
    21602160Jeff Triffo.<br>
     
    21752175<p>
    2176217693.
    2177 <b>Simplify volume data Python calls.</b>
     2177<strike><b>Simplify volume data Python calls.</b></strike>
    21782178<font color=green>Many improvements August 23, 2007</font><br>
    21792179Gabor Papai.<br>
     
    21862186<p>
    2187218792.
    2188 <b>Make multiscale tool work when atoms deleted.</b>
     2188<strike><b>Make multiscale tool work when atoms deleted.</b></strike>
    21892189<font color=green>Implemented October 25, 2008.</font><br>
    21902190Andy LiWang.<br>
     
    22062206<p>
    2207220790.
    2208 <b>Display 2-d contour lines on clipped volume surfaces.</b>
     2208<strike><b>Display 2-d contour lines on clipped volume surfaces.</b></strike>
    22092209<font color=green>Implemented September 9, 2008</font><br>
    22102210Yao Cong.<br>
     
    22442244<p>
    2245224588.
    2246 <b>Show map standard deviation.</b>
     2246<strike><b>Show map standard deviation.</b></strike>
    22472247<font color=green>Menu entry to print mean/SD values October 10, 2007</font><br>
    22482248Holland Cheng.<br>
     
    22822282<p>
    2283228384.
    2284 <b>Thicker silhouette edges.</b>
     2284<strike><b>Thicker silhouette edges.</b></strike>
    22852285<font color=green>Done July 28, 2007</font><br>
    22862286Tom Goddard<br>
     
    23322332<p>
    2333233381.
    2334 <b>Calculate density map for molecule.</b>
     2334<strike><b>Calculate density map for molecule.</b></strike>
    23352335<font color=green>Implemented January 14, 2008.</font><br>
    23362336Thomas Marlovits<br>
     
    23672367<p>
    2368236878.
    2369 <b>Path tracer markers.</b>
     2369<strike><b>Path tracer markers.</b></strike>
    23702370<font color=green>Implemented June, 2009</font><br>
    23712371Eric Pettersen<br>
     
    23932393<p>
    2394239476.
    2395 <b>Fetch EMDB maps.</b>
     2395<strike><b>Fetch EMDB maps.</b></strike>
    23962396<font color=green>Done Marc 11, 2009</font><br>
    23972397Cathy Lawson<br>
     
    24042404<p>
    2405240575.
    2406 <b>Fetch PQS biological assemblies.</b>
     2406<strike><b>Fetch PQS biological assemblies.</b></strike>
    24072407<font color=green>Implemented April 27, 2007</font><br>
    24082408Miguel Ortiz Lombardia<br>
     
    24442444<p>
    2445244571.
    2446 <b>Reoriented density maps.</b>
     2446<strike><b>Reoriented density maps.</b></strike>
    24472447<font color=green>Done for MRC and HDF formats September 4, 2007</font><br>
    24482448Tom Goddard<br>
     
    24542454<p>
    2455245570.
    2456 <b>Subsample volume data, netcdf.</b>
     2456<strike><b>Subsample volume data, netcdf.</b></strike>
    24572457<font color=green>Done with HDF, netcdf deprecated September 11, 2007</font><br>
    24582458Matt Baker<br>
     
    24652465<p>
    2466246669.
    2467 <b>HDF map file reader.</b>
     2467<strike><b>HDF map file reader.</b></strike>
    24682468<font color=green>Done August 7, 2007</font><br>
    24692469Matt Dougherty, Pawel Penczek<br>
     
    24782478<p>
    2479247968.
    2480 <b>Radial density plot.</b>
     2480<strike><b>Radial density plot.</b></strike>
    24812481<font color=green>Made radial density calculation script March 2, 2007</font><br>
    24822482Padma Natarajan<br>
     
    25012501<p>
    2502250266.
    2503 <b>Save BRIX format.</b>
     2503<strike><b>Save BRIX format.</b></strike>
    25042504<font color=green>Added BRIX writer October 19, 2007</font><br>
    25052505Christopher Akey<br>
     
    25112511<p>
    2512251265.
    2513 <b>User-defined surfaces.</b>
     2513<strike><b>User-defined surfaces.</b></strike>
    25142514<font color=green>Implemented January 30, 2008.</font><br>
    25152515Jeff Triffo<br>
     
    25412541<p>
    2542254262.
    2543 <b>Volume viewer code clean-up.</b>
     2543<strike><b>Volume viewer code clean-up.</b></strike>
    25442544<font color=green>Done August 9, 2007</font><br>
    25452545Tom Goddard<br>
     
    25502550<p>
    2551255161.
    2552 <b>Benchmark scores.</b>
     2552<strike><b>Benchmark scores.</b></strike>
    25532553<font color=green>Implemented May 2, 2008.</font><br>
    25542554Tom Goddard<br>
     
    25622562<p>
    2563256360.
    2564 <b>Color zone slider range.</b>
     2564<strike><b>Color zone slider range.</b></strike>
    25652565<font color=green>Implemented October 3, 2007.</font><br>
    25662566Jeff Triffo<br>
     
    25942594<p>
    2595259557.
    2596 <b>Slicing EM maps.</b>
     2596<strike><b>Slicing EM maps.</b></strike>
    25972597<font color=green>Resample volume added September 4, 2007</font><br>
    25982598Jeff Triffo<br>
     
    26252625<p>
    2626262654.
    2627 <b>Volume rendering memory use.</b>
     2627<strike><b>Volume rendering memory use.</b></strike>
    26282628<font color=green>Implemented September 6, 2008.</font><br>
    26292629Tom Goddard<br>
     
    26452645<p>
    2646264652.
    2647 <b>Update graphics driver bugs web page.</b>
     2647<strike><b>Update graphics driver bugs web page.</b></strike>
    26482648<font color=green>Done about once a year, May 2009</font><br>
    26492649Tom Goddard<br>
     
    26552655<p>
    2656265651.
    2657 <b>Crystal contacting chains.</b>
     2657<strike><b>Crystal contacting chains.</b></strike>
    26582658<font color=green>Partially done October 10, 2007
    26592659(<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/crystalcontacts/crystalcontacts.html">crystal contacts</a> tool).</font><br>
     
    26772677<p>
    2678267849.
    2679 <b>Unit cell outline box.</b>
     2679<strike><b>Unit cell outline box.</b></strike>
    26802680<font color=green>Meshmol command can serve October 10, 2007</font><br>
    26812681Sabuj Pattanayek<br>
     
    26872687<p>
    2688268848.
    2689 <b>Contouring optimization.</b>
     2689<strike><b>Contouring optimization.</b></strike>
    26902690<font color=green>New optimized algorithm October 2, 2007</font><br>
    26912691Tom Goddard<br>
     
    27132713<p>
    2714271446.
    2715 <b>Multiple volume dialogs.</b>
     2715<strike><b>Multiple volume dialogs.</b></strike>
    27162716<font color=green>Multiple volume histograms added August 10, 2007</font><br>
    27172717Basal Devkota<br>
     
    27402740<p>
    2741274143.
    2742 <b>Reading large maps.</b>
     2742<strike><b>Reading large maps.</b></strike>
    27432743<font color=green>Done July 31, 2007</font><br>
    27442744Irina Serysheva<br>
     
    27502750<p>
    2751275142.
    2752 <b>Collaboration descriptions.</b>
     2752<strike><b>Collaboration descriptions.</b></strike>
    27532753<font color=green>EMDB added 2009</font><br>
    27542754Tom Goddard<br>
     
    27592759<p>
    2760276041.
    2761 <b>Measure enclosed volume.</b>
     2761<strike><b>Measure enclosed volume.</b></strike>
    27622762<font color=green>Added keyboard shortcuts mv and ma September 29, 2006</font><br>
    27632763Tom Goddard<br>
     
    27692769<p>
    2770277040.
    2771 <b>Icosahedron surface session saving.</b>
     2771<strike><b>Icosahedron surface session saving.</b></strike>
    27722772<font color=green>Added December 5, 2008</font><br>
    27732773Tom Goddard<br>
     
    27782778<p>
    2779277939.
    2780 <b>IMOD file reader.</b>
     2780<strike><b>IMOD file reader.</b></strike>
    27812781<font color=green>Added to distribution October 5, 2007</font><br>
    27822782Masako Terada<br>
     
    27872787<p>
    2788278838.
    2789 <b>Image sequence file reader.</b>
     2789<strike><b>Image sequence file reader.</b></strike>
    27902790<font color=green>Added TIFF stack reader July 21, 2007</font><br>
    27912791William Beaver<br>
     
    28052805<p>
    2806280636.
    2807 <b>Make chains become separate molecules.</b>
     2807<strike><b>Make chains become separate molecules.</b></strike>
    28082808<font color=green>Added to distribution October 10, 2007</font><br>
    28092809Elaine Meng<br>
     
    28162816<p>
    2817281735.
    2818 <b>Delphi Controller surface coloring.</b>
     2818<strike><b>Delphi Controller surface coloring.</b></strike>
    28192819<font color=green>Implemented April 25, 2007.</font><br>
    28202820Elaine Meng<br>
     
    28352835<p>
    2836283633.
    2837 <b>Surface coloring key.</b>
     2837<strike><b>Surface coloring key.</b></strike>
    28382838<font color=green>Implemented July 15, 2008.</font><br>
    28392839Alexander Rusnak<br>
     
    28442844<p>
    2845284532.
    2846 <b>Movie recorder format compatibility.</b>
     2846<strike><b>Movie recorder format compatibility.</b></strike>
    28472847<font color=green>Powerpoint movie fixes documented March 2, 2007</font><br>
    28482848Tom Goddard<br>
     
    28842884<p>
    2885288528.
    2886 <b>Mask volume with cylinder.</b>
     2886<strike><b>Mask volume with cylinder.</b></strike>
    28872887<font color=green>Implemented October 17, 2007
    28882888(<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html">mask</a>
     
    29062906<p>
    2907290726.
    2908 <b>Buried surface area.</b>
     2908<strike><b>Buried surface area.</b></strike>
    29092909<font color=green>Added measure command January 2009</font><br>
    29102910Tom Goddard<br>
     
    29272927<p>
    2928292824.
    2929 <b>Electrostatic potential coloring.</b>
     2929<strike><b>Electrostatic potential coloring.</b></strike>
    29302930<font color=green>Similar fix made May 6, 2008.</font><br>
    29312931Elaine Meng<br>
     
    29382938<p>
    2939293923.
    2940 <b>MSMS surface calculation with stand-alone program.</b>
     2940<strike><b>MSMS surface calculation with stand-alone program.</b></strike>
    29412941<font color=green>Implemented March 18, 2008.</font><br>
    29422942Tom Goddard<br>
     
    29492949<p>
    2950295022.
    2951 <b>Surface model selection inspector.</b>
     2951<strike><b>Surface model selection inspector.</b></strike>
    29522952<font color=green>Implemented January 8, 2008.</font><br>
    29532953Tom Goddard<br>
     
    29912991<p>
    2992299218.
    2993 <b>Mask map to icosahedron.</b>
     2993<strike><b>Mask map to icosahedron.</b></strike>
    29942994<font color=green>Mask command October 17, 2007</font><br>
    29952995Wen Jiang, Gabe Lander<br>
     
    30013001
    3002300217.
    3003 <b>Masking within any surface.</b>
     3003<strike><b>Masking within any surface.</b></strike>
    30043004<font color=green>Mask command October 17, 2007</font><br>
    30053005Tom Goddard<br>
     
    30113011<p>
    3012301216.
    3013 <b>Volume solid rendering improvements.</b>
     3013<strike><b>Volume solid rendering improvements.</b></strike>
    30143014<font color=green>New transparency blending August 2, 2007</font><br>
    30153015Sebastian Haase<br>
     
    30303030<p>
    3031303114.
    3032 <b>Determine map symmetries.</b>
     3032<strike><b>Determine map symmetries.</b></strike>
    30333033<font color=green>Fit map prints rotation axis/angle/shift February 28, 2007</font><br>
    30343034Tom Goddard<br>
     
    30413041<p>
    3042304213.
    3043 <b>EMDB / PDB fitting.</b>
     3043<strike><b>EMDB / PDB fitting.</b></strike>
    30443044<font color=green>Fetch EMDB maps and fit PDBs March 11, 2009</font><br>
    30453045Richard Newman, Cathy Lawson<br>
     
    30613061<p>
    3062306211.
    3063 <b>Put old plugins on web.</b>
     3063<strike><b>Put old plugins on web.</b></strike>
    30643064<font color=green>Volume stats distributed October 3, 2007</font><br>
    30653065Tom Goddard<br>
     
    30713071<p>
    3072307210.
    3073 <b>Chimera web page for electron microscopy.</b>
     3073<strike><b>Chimera web page for electron microscopy.</b></strike>
    30743074<font color=green><a href="http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html">Volume guide</a> created 2007</font><br>
    30753075Tom Goddard<br>
     
    30993099<p>
    310031007.
    3101 <b>Surface smoothing.</b>
     3101<strike><b>Surface smoothing.</b></strike>
    31023102<font color=green>Fixed by using gradient normals, October 6, 2007</font><br>
    31033103Tom Goddard, Steve Ludtke<br>
     
    31193119<p>
    312031205.
    3121 <b>Surface display optimization.</b>
     3121<strike><b>Surface display optimization.</b></strike>
    31223122<font color=green>Implemented June 6, 2008.</font><br>
    31233123Tom Goddard<br>
     
    31323132<p>
    313331334.
    3134 <b>Ellipsoid molecule display.</b>
     3134<strike><b>Ellipsoid molecule display.</b></strike>
    31353135<font color=green>Measure inertia command Implemented July 24, 2009.</font><br>
    31363136Tom Goddard<br>
     
    31443144<p>
    314531453.
    3146 <b>Fetch by ID save button.</b>
     3146<strike><b>Fetch by ID save button.</b></strike>
    31473147<font color=green>Fetch download directory added March 10, 2009.</font><br>
    31483148Tom Goddard<br>
     
    31643164<p>
    316531651.
    3166 <b>Fetch EDS maps.</b>
     3166<strike><b>Fetch EDS maps.</b></strike>
    31673167<font color=green>Implemented April 27, 2007</font><br>
    31683168Tom Goddard, forgot user<br>