Thanks, Phil. Yes, I missed that.
http://www.rcsb.org/pdb/files/1crn.pdb
has moved, but
http://www.rcsb.org/pdb/files/ligand/hem
has not.
I will get that out later tonight.
On Mon, Apr 11, 2016 at 8:50 PM, Philip Bays <pb...@saintmarys.edu> wrote:
> 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
>
>
> 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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> Applications Manager provides deep performance insights into multiple
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> your business applications. It resolves application problems quickly and
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>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department 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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your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
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