[had a few important bug fixes on this already; re-released as Jmol
13.1.16a]
On Thu, Jun 6, 2013 at 12:46 AM, Robert Hanson <hans...@stolaf.edu> wrote:
> Jmol 13.1.16 contains many new features and several bug fixes. It will be
> particularly of interest to those who use PyMOL.
>
> JmolVersion="13.1.16"
>
> new feature: color BALLS
> -- distinct from color ATOMS because it doesn't get inherited
> -- for PyMOL compatibility with sphere_color
>
> new feature: restore SCENE "xxxx" nSec
>
> new feature: Scene menu
> -- PyMOL scene names, in order
>
> new feature: added parameters to moveTo allows setting cameraDepth,
> cameraX, and cameraY
>
> new feature: moveTo <nseconds> PYMOL [18-element standard PyMOL view
> matrix]
> -- used for PSE file loading
> -- to be used also for scenes
> [0-8] are 3x3 rotation matrix (row/column inverted)
> [9,10] are x,y translations (y negative)
> [11] is distance from camera to center (negative)
> [12-14] are rotation center coords
> [15-16] are slab and depth distance from camera (0 to ignore)
> [17] is field of view; positive for orthographic projection
>
> new feature: cache CLEAR
> -- same as cache REMOVE ALL
>
> new feature: load xxx.pse FILTER "DOCACHE"
> -- specifically for editing large PSE files when included in a state
> -- caches streamlined file that is still readable by PyMOL (needs
> testing!)
> (no electron density map data, for instance -- see HupA_2.pse)
> -- caches all isosurfaces, creating JVXL equivalents
> -- should be followed with WRITE xxx.pngj or WRITE xxx.jmol or WRITE
> xxx.zip
> -- for example:
> before:
> 04/07/2013 07:46 AM 11,929,507 HupA_2.pse
>
> $ zap;load SYNC "file:///C:/temp/downloads/HupA_2.pse" filter 'DOcache'
> $ write t.zip
>
> after:
> Listing archive: t.zip
> Physical Size = 395174
>
> Date Time Attr Size Compressed Name
> ------------------- ----- ------------ ------------
> ------------------------
> 2013-05-17 06:46:36 ..... 1092432 219718 HupA_2.pse
> 2013-05-17 06:46:36 ..... 1473760 6589
> isosurface_level2
> 2013-05-17 06:46:36 ..... 25495 11624 state.spt
> 2013-05-17 06:46:36 ..... 134 119
> JmolManifest.txt
> 2013-05-17 06:46:36 ..... 0 2
> Jmol_version_13.1.16_dev_2013.05.17__2013-05-15_07.09
> 2013-05-17 06:46:36 ..... 158082 156316 preview.png
> ------------------- ----- ------------ ------------
> ------------------------
> 2749903 394368 6 files, 0
> folders
>
> new feature: anim FRAMES [1, 3, 9, 9, 9, 3, 1]
> -- arbitrary PyMOL-like model list
>
> new feature: FRAME n
> -- same as MODEL n, unless we have PyMOL-like frames
> -- if have frames, then FRAME 2 goes to the second frame (model 3 in
> this case)
> -- MODEL n still always goes to a specific model.
> -- all relative options -- FIRST LAST PREV NEXT -- refer to frames if
> there are frames
> even if the MODEL command is given.
>
> new feature: pyMOL PSE state options: LOAD "FOO.PSE" state FILTER "xxxx"
> -- [state not present; default] load all PyMOL states (one PyMOL state
> == one Jmol model)
> -- state = 0 (load only the current PyMOL state)
> -- state > 0 (load just a specific PyMOL state)
> -- FILTER "nosurface" -- load PyMOL file without surfaces
> -- FILTER "
>
> new feature: getProperty BONDINFO {atomset1} {atomset2}
>
> new feature: measurements with IDs and radius/diameter:
> -- measure ID "xxx" ...
> -- measure ID "xxx" RADIUS x.y (or DIAMETER x.y)
> -- renders as dots
>
> new feature: set zoomHeight
> -- FALSE by default
> -- set TRUE for PyMOL-like resizing (scale only set by height
> adjustment)
>
> new feature: isosurface color density (decimal)
> - variable decimal point size
>
> new feature: PyMOL CGOs as CGO command
> - needs testing
> - CGO ID "xxx" [ cgo data (float array) ]
> - includes basic CGO methods
> BEGIN
> GL_POINTS
> GL_LINES
> GL_LINESTRIP
> GL_TRIANGLE
> GL_TRIANGLE_STRIP
> GL_TRIANGLE_FAN
> VERTEX
> END
> COLOR
> NORMAL
> SIMPLE_LINE
> SAUSAGE
> TRICOLOR_TRIANGLE
>
> popup: added menu for MEP range -0.1 0.1
>
> PyMOL: uniqueBondSettings working
>
> PyMOL: better scene restore;
>
> PyMOL: adds SASURFACE option (surface_solvent ON), with "carving"
> (ProFusion_ABL.pse, scene F6)
>
> PyMOL: abstraction of scene setting from reader
>
> PyMOL: first phase of reader development complete (working with Jaime
> Prilusky)
> -- 104 test models http://ispcsrv3.weizmann.ac.il/a2jmolb/browse
> -- implementation of standard objects, including:
> -- atoms with labels
> -- bonds
> -- standard PyMOL rendering, including:
> -- lines
> -- sticks
> -- nonbonded (stars)
> -- nb_spheres
> -- cartoons of various types (not plank)
> -- rockets
> -- ribbon (backbone/trace)
> -- putty (trace)
> -- dots
> -- measures
> -- simple CGO objects
> -- molecular surfaces
> -- electron density as points and meshes
> -- custom colors
> -- fog and slab
> -- morphing movies
> -- JVXL caching of isosurfaces
>
> PyMOL: measurement font/offsets enabled
> -- adds measure ID "xxx" FONT scale face style
> -- adds measure ID "xxx" OFFSET [mode, sx, sy, sz, ax, ay, az]
> -- adds measure ID "xxx" OFFSET {sx, sy, sz}
>
> PyMOL: perspective fix for translated center -- H115W.PinM.PSE
>
>
> bug fix: JavaScript: adding SYNC
> bug fix: antialiasing or resizing stray lines problem solved (introduced
> in 11.0, 08/2006!)
> bug fix: "display add" by itself should not do anything
> bug fix: Hall translation initialization problem
> bug fix: JavaScript reading of old-style JVXL files
> bug fix: Gaussian reader not splitting MO set by model
> bug fix: polyhedron reading from state
> bug fix: connect delete not saved in state
> bug fix: rockets not working for alpha polymer (also in 13.0.16)
> bug fix: GXL added to carbohydrates
> bug fix: show state/anim turns "anim" into "animation"
> bug fix: MoldenReader orbitals are not in energy order; use FILTER
> "NOSORT" to prevent sorting by energy
> bug fix: simultaneous spin/animation broken in 13.1.13
> bug fix: MoldenReader fix for file blank lines and g,h,i orbitals - also
> for 13.0.16
> bug fix: COMPARE does not allow nSeconds at beginning, as described in
> documentation
> bug fix: isosurface VOLUME/AREA SET n cannot return to full array
> reporting; SET -1 added.
> bug fix: isosurface VOLUME/AREA always returns an array, possibly of
> length 0
> bug fix: isosurface molecular/solvent can give inappropriate inner surfaces
> bug fix: show selected includes deleted atoms
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
How ServiceNow helps IT people transform IT departments:
1. A cloud service to automate IT design, transition and operations
2. Dashboards that offer high-level views of enterprise services
3. A single system of record for all IT processes
http://p.sf.net/sfu/servicenow-d2d-j
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
