Just on an initial superficial test with both jsmol.htm and test2.htm. Heme
does not load. Get an unrecognized file type. Works fine in the 0331 update.
Other RCSB links work fine.
Safari and Firefox on Mac on local network.
Phil
> On Apr 11, 2016, at 7:44 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
> Jmol.___JmolVersion="14.4.4_2016.04.11"
>
> bug fix: qchem reader fails to switch to spherical D/F basis for second
> structure
> bug fix: pointGroup secondary axis in yellow is too hard to see -- using
> "orange" instead
>
>
> new feature: symop() options:
> symop(op)
> -- returns the 4x4 matrix representation of this operator
> symop(op, atom)
> -- returns the point generated by operator op on atom
> -- op may be a positive or negative integer indictating the operation (or
> its reverse)
> to apply from the loaded space group -- for example, symop(3, @1) or
> symop(-4, {atomindex=16})
> -- op may be a string such as "x+1/2,1/2-y,z" representing a specific
> generic operation
> symop(atom1, atom2)
> -- returns the description of the first of possibly several operations
> that take atom1 to atom2, for example:
> "2-fold screw axis|translation: 1/2 0 0"
> symop(atom1, atom2, n)
> -- returns the description of the nth operation that takes atom1 to atom2
> symop(...point...)
> -- any place an atom can be used in symop(), one can substitute an xyz
> coordinate.
> -- for example, symop(@1, {1/2 1/2 1/2})
> {atomset}.symop(...)
> -- when more than one model is loaded, prepending any symop function with
> an atom set specifies which
> atoms, space group, and unit cell are being referenced. For example,
> {2.1}.symop(5) operates only on
> atoms in the first model of the second loaded file, using the
> appropriate space group and unit cell.
> In this way, "@1" will designate one atom only, provided only one
> model is showing (using the FRAME/MODEL command).
> If only one model has been loaded, there is no need to use this
> syntax; symop(...) will do the same.
> symop(..., outputType)
> -- All uses of symop() and {atomset}.symop() can be extended using a final
> parameter that
> changes the default output described above to be something else. Options
> for outputType include:
>
> "draw" Returns the Jmol script illustrating this operation with DRAW
> commands.
>
> $ print symop(3,"draw")
> draw ID draw_* delete
> draw ID draw_frame1X diameter 0.15{5.5172 1.9683 2.7802}{6.5172
> 1.9683 2.7802} color red
> ...
>
> "full" Returns the tab-separated Jones-Faithful string and descriptor
> for this operation.
>
> $ print symop(3,"full")
> -x,-y,-z(mx,my,mz) Ci: 0 0 0
>
> "lattice" Returns the lattice type associated with the space group
> involving this operation.
>
> "list" Specifically when two atoms or points are specified, returns a
> string list of all operations
> taking the first to the second.
>
> $ print symop(@3,@21,"list")
> 5 x+1/2,-y+1/2,-z+1/2(-mx,my,mz) 2-fold screw
> axis|translation: 1/2 0 0|time-reversed
> 7 -x+1/2,y+1/2,z+1/2(-mx,my,mz) n-glide plane|translation:
> 0 1/2 1/2|time-reversed
>
> Note that this string can be turned into a standard array
> using .lines.split("\t",true):
>
> $ print symop(@3,@21,"list").lines.split("\t",true)
> [
> 5
> x+1/2,-y+1/2,-z+1/2(-mx,my,mz)
> 2-fold screw axis|translation: 1/2 0 0|time-reversed
> ]
> [
> 7
> -x+1/2,y+1/2,z+1/2(-mx,my,mz)
> n-glide plane|translation: 0 1/2 1/2|time-reversed
> ]
>
> "array" Returns an associative array that contains critical
> information relating to this operation.
>
> $ load =magndata/0.34
> $ print symop(3,"array")
> {
> "inversionCenter" : {0.0 0.0 0.0}
> "label" : "Ci: 0 0 0"
> "matrix" :
> [
> [-1.0, 0.0, 0.0, 0.0]
> [0.0, -1.0, 0.0, 0.0]
> [0.0, 0.0, -1.0, 0.0]
> [0.0, 0.0, 0.0, 1.0] ]
> "timeReversal" : 1
> "xyz" : "-x,-y,-z(mx,my,mz)"
> "xyzOriginal" : "-x,-y,-z,m"
> }
>
> In addition, all possible keys of this array may be used as well for
> outputType. These include:
>
> "axisVector", "cartesianTranslation", "centeringVector",
> "fractionalTranslation",
> "inversionCenter", "label", "matrix", "plane", "rotationAngle",
> "timeReversal", "unitTranslation", "xyz", and "xyzOriginal"
>
> Three of these that may be less than obvious are explained below:
>
> "centeringVector" For operations that are pure lattice translations,
> returns the vector
> for this centering in fractional coordinates.
>
> "timeReversal" This quantity is 0 for standard space groups.
> Magnetic space group
> operations also include the possibility of inversion
> of the spin
> along with any 3D symmetry operation. This inversion
> characteristic
> is referred to as "time reversal" and takes the value
> of 1 or -1.
>
> "unitTranslation" Symmetry operations involving two atoms may include
> an extra
> lattice translation if the two atoms are in different
> unit cells.
> This translation is above and beyond any fractional
> lattice centering
> that this operator incorporates for a face- or
> body-centered space group.
>
> new feature: show spacegroup/xxxxx
>
> -- selects lines from a space group report similar to the way show
> state/xxxx works
> -- example:
>
> load =ams/quartz 1
> show spacegroup/Class
>
> new feature: show/draw symop @1 @2
> -- gives full list of matching symmetry operations
> -- example:
>
> $ load =magndata/1.23 {444 555 1} packed
> $ show symop @153 @299
>
> 1 x+2,y,z2(mx,my,mz) translation: 2 0 -2
> 5 -x,-y,-z(mx,my,mz) Ci: 0 0 0
> 11 x+2,-y,-z(-mx,my,mz) 2-fold screw axis|translation: 2 0
> 0|time-reversed
> 15 -x,y,z2(-mx,my,mz) c-glide plane|translation: 0 0
> -2|time-reversed
>
> new feature: show/draw symop @1 @2 n
> -- shows or draws the nth symmetry operation relating atom 1 to atom 2
> -- example:
>
> $ load =magndata/1.23 {444 555 1} packed
> $ show symop @153 @299 3
>
> 11 x+2,-y,-z(-mx,my,mz) 2-fold screw axis|translation: 2 0
> 0|time-reversed
>
> new feature: print pointgroup("spacegroup", @1)
> -- analyzes the point group (crystal class) of a crystal.
> -- uses three irrational-coordinate points to generate all possible operators
> -- creates a map with keys (somewhat variable depending upon axes present):
>
> C2
> C3
> Ci
> Cs
> S6
> detail
> distanceTolerance
> linearTolerance
> nAtoms
> nC2
> nC3
> nCi
> nCn
> nCs
> nS6
> nSn
> nTotal
> name
> points
> principalAxis
>
> new feature: draw SPACEGROUP
> -- draws all operations in space group
>
> new feature: draw POINTGROUP SPACEGROUP
> -- draws crystal class symmetry operations for a space group
> -- uses point group style, with circular planes
>
> new feature: @1.find("crystalClass", pt)
> -- generates a list of points based on a model's crystal class (point group)
> -- uses @1 just to find the unit cell and space group
> -- optional pt is used as a generator (defaults to @1)
> -- example:
> load =ams/calcite 1
> x = @3.find("crystalClass")
> print pointgroup(x).name
> draw points @x
> polyhedra ID p {0 0 0} to @x
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr <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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Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu
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