[Jmol-users] Jmol 16.2.3 - bug fixes and MODELKIT SPACEGROUP

[Robert H. <ha...@st...>]

With this version
<https://sourceforge.net/projects/jmol/files/Jmol/Version%2016.1/Jmol%2016.2.3/>,
the space group upgrade for Jmol is essentially complete.

[image: 84-84.png]
[PNGJ illustrating two settings of space group 84 (P 4/2 m). The one
outlined in red is the standard unit cell; the larger one is one of its
subgroups of index 2 (because we have lost half of the diagonal
translations -- note that the vertical 2-fold axes are only half the
density in the yellow subset cell on the right).

- Jmol now has access to the full Bilbao Crystallographic Server (BCS)
collection of 611 standard and nonstandard space group settings (plus a
couple more). It is possible to add customized settings or just create them
on the fly.
- Jmol uses these settings natively; they are built into Jmol as
(potentially user-modifiable) JSON property files
- Jmol can generate and visualize any nonstandard space group setting based
on a standard setting using simple "(P,p)" transformation notation.
- You can switch settings after loading a structure, seeing how the
symmetry (but not the structure itself!) changes with different unit cells,
for example.
- You can build models from scratch in any space group setting.
- Jmol has the full complement of standard BCS group-maximal subgroup
transformations up to index 4 (3767 total). The full collection of
visualizations of these relationships as PNGJ model files is available at
https://chemapps.stolaf.edu/jmol/data/ita/subgroups.zip (190M). These can
be dropped into Jmol or viewed as a gallery after downloading to your
machine.
- Combined with the nonstandard settings, Jmol can calculate and visualize
any *non*-standard group-maximal subgroup transformation up to index 4.
- Combined with multiple settings, Jmol can calculate and visualize any
group-subgroup chain of transformations.
- All the matrix math associated with these calculations can be carried out
and demonstrated easily using Jmol scripting.

Several additional new features and bug fixes:

Jmol.___JmolVersion="16.2.3" // (legacy) also 16.2.4 (swingJS)

demo page: https://chemapps.stolaf.edu/jmol/jsmol/iucrdemo
  -- supplement to a forthcoming publication
  -- lots of examples of using the MODELKIT SPACEGROUP command

note: completion of the MODELKIT SPACEGROUP implementation initiated in
15.2.30/14.2.30

bug fix: (JavaScript) no spinner showing at startup.
                      Jmol_spinner.gif was missing in site/jsmol/j2s/img

bug fix: (JavaScript chemapps) the php/jsmol.php AJAX relay was failing due
to
                               the presence of both
header('Access-Control-Allow-Origin: *') in jsmol.php
                               and .htaccess file in site/, causing a
"multiple header" error.
                               The .htaccess file was kept, and the php
header was removed.

bug fix: (legacy JavaScript only) right-click on pop-up menu throws
background error
                                  and fails to place submenu correctly
                                  (traced to minor jMenu incompatibility
with jQuery 3.7.1)

bug fix: (JavaScript) Jmol javascript command containing call back to
Jmol.script()
                           fails to execute callback script

bug fix: (JavaScript) JSpecView and other pages fail to open due to Enum
and
                           ArrayList coding bugs recently introduced that
are only used in JSpecView

bug fix: animation range not responsive to load append

bug fix: PDB reader needs to allow PDB files with BIOMT but no CRYST1/SCALE
headers

bug fix: SHELX reader fails due to LATT processing failure

bug fix: display of symmetry elements in SHOW and DRAW minor issues

bug fix: DRAW UNITCELL with {555 666 1} notation should show all interior
edges of
         block of cells

bug fix: more work on subgroup-group relations
 - still finalizing code for using transformations such as
"a+b,a-b,c;1/2,1/2,0"
 - for example, to create a group, add atoms, and display a packed
subgroup, coloring by site:

zap
modelkit spacegroup 18
draw unitcell color red
modelkit add P wyckoff "G"
modelkit spacegroup "18 >c,a,b;0,1/4,0>4" packed
color property site
draw spacegroup all


feature change: DRAW UNITCELL default changed to MESH NOFILL
 - was normal default of FILL NOMESH, but this is much better
 - overridden by explicit NOMESH or FILL
 - does not affect states, as they are explicit, not default

feature change: x = spacegroup("153") or x = spacegroup(153)
 - one parameter, just a number from 1 to 230
 - was Jmol's idiocyncratic Hall-notation-derived operator list
 - now ITA standard list
 - same list; just a different order
 - spacegroup() by itself shows current, possibly file-derived, operators.

new feature: x = spacegroup("153:")
 - with colon
 - returns Jmol's internal setting and original listing

new feature:  DRAW UNITCELL AXES
 - draws axes red/green/blue (no labels) with unit cell.

new feature: spacegroup(g1,g2,i1,i2)
 - same as spacegroup(g1,g2,i1,i2,"subgroups")
 - "subgroups" is unnecessary

new feature: x = spacegroup("Hall:p 32 2\" (0 0 2)")
 - translates Hall notation to XYZ list
 - outputs a map similar to x = spacegroup(154) with at least
   keys HallSymbol, operationCount, and operationsXYZ;
   possibly, if known, also:

   HermannMauguinSymbol
clegId
crystalClass
ita
itaIndex
jmolId


new feature: x = {*}.rxyz
 - returns rational fraction if within +/- 0.001 of n/2,3,4,6,8,12,24,48
 - returns rounded to 0.001 if not
 - string value with parentheses: "(1/2 1/2 1/2)"

new feature: fpt.rxyz
 - returns rational of fractional.
 - {1/2 1/2 1/2}.rxyz == "(1/2 1/2 1/2)"

new feature: x = matrix(...)
  - creates a 3x3 or 4x4 matrix
  - options include (by example):
 matrix("x-y+1/2,x+y,z")     // row-based
 matrix("a+b+1/2,b-a,c")     // column-based
 matrix("a+b,b-a,c;1/2,0,0") // ITA transform notation, col-based
 matrix([1,2,3,4,5,6,7,8,9]) // 3x3 from array[9]
 matrix([1,2,3,4,5,6,7,8,9,0,1,2,3,4,5,6]) // 4x4 from array[16]
 matrix([1,2,3] [4,5,6] [7,8,9]) // 3x3 from array[3][3]
 matrix([1,2,3,4] [5,6,7,8] [9,0,1,2] [3,4,5,6]) // 4x4 from array[4][4]

      P = matrix("c,a,b;1/2,0,0");
      f = {0.5 0.25 0.5};
      print P*f;

         {0.75 0.5 0.5}

new feature: x = matrix(..., "abc")
new feature: x = matrix(..., "xyz")
  - returns the string form of a 4x4 matrix, either in abc-column format or
xyz-row format

new feature: MODELKIT SPACEGROUP <setting>
 - Jmol will automatically adjust unit cell if necessary.
 - should be used after ZAP or LOAD
 - for example:

function test(n,i) {
if (!i) {
load @{"=aflowlib/" + n} + " packed";
center unitcell;
print "nSettings=" +  spacegroup("ITA/" + n).n;
test(n,1);
} else {
draw delete;
modelkit spacegroup @{"" + n + "."+i} packed;
draw ID @{"sg"+i} spacegroup all;
center visible;
axes 0.1;
connect auto;
moveto axis c1;
}
}

  test(23)

  opens an example AFLOW Encyclopedia of Crystallographic Prototypes, then
  switches to a one of the available settings, packing the new unit cell
    and displays all symmetry operations. Finally, does some clean up and
    goes to the standard ITA "c1" axis view. (looing toward 0 along c axis
in the top left corner)

new feature: MODELKIT SPACEGROUP "n >sub> m"
  - switch from crystallographic group to maximal subgroup
  - uses (unpublished) CLEG notation (more details to follow)
  - chooses first-listed transformation
  - typically a translationengleichen (translation-preserving)
transformation

  - for example: MODELKIT SPACEGROUP 13 >sub> 10

function showSubgroup(i1, i2) {
 if (!i2) {
print spacegroup(i1,0,"subgroups");
return;
 }
 save orientation o1;
 zap;
 modelkit spacegroup @i1;
 restore orientation o1;
 center unitcell;
 draw uc1 unitcell color red;
 draw sg1 spacegroup all;
 modelkit add P wyckoff "G";
 modelkit spacegroup @{"" + i1 + ">sub>" + i2} packed;
 color property site;
 draw uc2 unitcell color yellow;
 draw sg2 spacegroup all;
 delay 2;
 for (var i = 0; i < 10; i++) {
delay 1;
draw sg1* on;
draw sg2* off;
delay 1;
draw sg1* off;
draw sg2* on;
 }
 draw sg1* on;
 draw sg2* on;
}

    showSubgroup 107
    showSubgroup 107 42

new feature: unitcell NONE
 - removes unit cell and spacegroup
 - removes unit cell and spacegroup information from model auxiliary info _M
 - allows nonperiodic manipulation of atom positions

new feature: SHELX reader returns Q-peaks as "Xx" (unknown atom); was
returning "C"

new feature: x = spacegroup("ITA/4:c,a,b")
 - finds the ITA spacegroup setting with this specific transformation.
 - text match so must be exact form:
  [rotation;translation], e.g. a,b,c;0,0,0
    "2/3a+1/3b+1/3c,-1/3a+1/3b+1/3c,-1/3a-2/3b+1/3c"
"a+b,-a+b,c;-1/4,-1/4,-1/4"

new feature: x = spacegroup(itaNo, itaFrom, index1, index2, "subgroups")
 - returns information on group-subgroup relationships
 - based on Bilbao Crystallographic Server public data
 - uses set of JSON data files - see
 - return depends upon values:

     spacegroup(4,"subgroups")       // all maximal subgroup data for space
group 4
spacegroup(4,0,"subgroups")     // an array of known subgroup numbers
     spacegroup(4,5,"subgroups") // list of all 4 >> 5
     spacegroup(4,5,1,"subgroups")   // first-listed 4 >> 5 as a map
     spacegroup(4,0,2,"subgroups")   // second listed subgroup as a map
     spacegroup(4,0,2,1,"subgroups") // second listed subgroup, first
transformation
     spacegroup(4,5,1,2,"subgroups") // first listing for 4>>5, second
transformation
     spacegroup(4,0,0,0,"subgroups") // an array of arrays of [isub, ntrm,
subIndex, type]

  where

   *  [ isub, ntrm, subIndex, idet, trType ]
   *
   *  isub: subgroup ITA number
   *  ntrm: transformation count
   *  subIndex: index of this group-subgroup relationship
   *  idet:  determinant if determinant >= 1; -1/determinant if determinant
< 1
   *  trType: 1 translationengelieche,
   *          3 klassengleiche "ct" loss of centering translation,
   *          4 klassengleiche "eu" enlarged unit cell

-- 
Robert M. Hanson
Professor of Chemistry, Emeritus
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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