Jmol users ---
Ah, for those 258 people who downloaded 13.2.4 or 13.3.4, just to let you
know, the SELECT command is broken for proteins:
select 1-3 // (with no chain identifier)
will return 0 atoms selected
13.2.4 and 13.3.4 have been uploaded. Check for a date of 23-8-2013 under
...about on the pop-up menu.
Sorry about that. This bug was introduced June 27, I believe, when I added
support for multi-character chains in mmCIF files.
Thanks very much to Shannon Colton at Milwaukee School of Engineering for
tipping me off to this.
Bob
On Thu, Aug 22, 2013 at 3:15 PM, Robert Hanson <[email protected]> wrote:
> See https://sourceforge.net/projects/jmol/files/
>
> There is a feature change:
>
> FEATURE CHANGE: set wireframeRotation expanded to include bioshapes and
> isosurfaces
>
> Bug fixes in 3.2.4 and 3.3.4:
>
> bug fix: set wireframeRotation not working ("inMotion" flag not properly
> read in Viewer).
> bug fix: CIF reader not processing _ccdc_geom_bond_order records
> bug fix: File dialog problems with paths having space
> bug fix: GAMESS reader not reading energies
> bug fix: TRY failure in a load command followed by a successful load
> having a loadScript will pop past the second TRY and crash
> Jmol
> bug fix: translation not read from state
> bug fix: CIF reader does not find Hall name for space groups
> bug fix: binding names not included in SHOW MOUSE
> bug fix: "single" touch can fire double-click
> bug fix: {x}.tensor() command fails when no atom tensors
> bug fix: screen repaints were being requested far too frequently
> bug fix: set loglevel 6 (debugHigh) not working
> bug fix: {*}.tensor("", "id") not implemented
> bug fix: {*}.tensor("") not implemented
> bug fix: {*}.tensor("adp") fails
> bug fix: {*}.symmetry fails when space group is P1
> bug fix: atom tensors lost when merging
> bug fix: float parser broken in dev_2013.08.07
> bug fix: zoom setting lost in state
> bug fix: shapeInfo not reporting visibility of isosurface
> bug fix: filter lost after CENTROID or PACKED load option
> bug fix: set rangeSelected not functional
> bug fix: minimization can fail after MMFF switches to UFF.
> bug fix: CIF reader fix for no element given "phenyl1" in ZjzxlegN.cif
>
> New Features in 3.3.4:
>
>
> new feature: set platformSpeed [0 to 10]
> -- basically an expanded "set wireframe OFF" with more options
> -- only effected during model rotation
> (including mouse dragging, spin, vibration, and animation)
> -- default value is 10 (all features; no compromises)
> -- value >= enables
> 8 antialiasDisplay (and thus, all features)
> 7 translucency
> 6 meshes (contact, draw, isosurface, MO, pmesh,
> lcaocartoon, CGO)
> 5 cartoons, rockets, trace, ribbon
> 4 geosurfaces
> 3 ellipsoids
> 2 wireframe and balls
> 1 none of the above (same as "set wireframeRotation
> off")
> 0 [reserved for "auto"]
>
> new feature: rotate BEST
> new feature: rotate SELECTED BEST
>
> new feature: quaternion("best")
> -- delivers actual quaternion
>
> new feature: pop-up menu selection "view...best"
>
> new feature: show ROTATION BEST
> -- operates on currently selected atoms
> -- reports "{quaternion}"
>
> new feature: show ROTATION VOLUME
> -- calculates approximate best box (from 1495 quaternion-based
> alternatives)
> -- reports "<volume> {dx dy dz}"
> -- where <volume> is the volume,
> -- and {dx dy dz} are the dimensions, where dx > dy > dz
>
> new feature: COMPARE {atoms} [coords]
> new feature: COMPARE {atoms} ATOMS {subset1} [coords1] {subset2} [coords2]
> ...
>
> new feature: _logfile holds full path to logfile
>
> new feature: reading of incommensurate modulated crystal structures:
> new feature: Jana2006 M40/M50 file reading
> new feature: MODULATION command -- for modulated structures
> -- operates on currently selected set of atoms
> -- MODULATION ON
> -- MODULATION OFF
> -- MODULATION t
> -- sets modulation "t" of selected atoms
> -- MODULATION PLAY t1 t2
> -- animates a once-through sequence of t from t1 to t2
> -- MODULATION FPS x.x // may be < 1
> -- sets speed of animation
> new feature: Jana2006 reader -- reader for http://jana.fzu.cz/
> new feature: CIF reader reads incommensurate modulated structures
> -- FILTER options include:
> -- NOSPECIAL (include special atoms for debugging
> -- MODAVERAGE (do not read modulation
> -- MODAXES=xyz (select only specific axes -- x, y, and/or z)
> -- MODVIB (set positions to average, but enable modulation as if
> vibration
> -- NOSYM (no symmetry read)
>
>
>
>
>
>
>
> --
> 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
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