Just updated to 13.2.4, and I'm having a couple of problems.

First, loading PDBs using "load =XXXX" doesn't seem to work on Safari or Google Chrome (OS X 10.8.4). Try File > Load PDB Structure on this page: Looking at it, I think I've traced the problemůmy page is trying to use jsmol.php on your server. How do I set JSmol up to use jsmol.php in my own copy of JSmol? If it's any help, loading up compounds by name works fine.

I see a weird error in the JS console when the page loads: "GET 404 (Not Found)"--maybe a .map where a .js should be?

Cheers, Mike

Michael Evans
Freshman Chemistry Lab Coordinator
Georgia Institute of Technology
(502) 439-2540 |

On Aug 23, 2013, at 1:44 PM, Robert Hanson <> wrote:

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.


On Thu, Aug 22, 2013 at 3:15 PM, Robert Hanson <> wrote:
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 ""

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
    -- sets modulation "t" of selected atoms
    -- 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
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

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

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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