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[Jmol-commits] SF.net SVN: jmol:[22690] trunk/Jmol/src/org/jmol/view er/Jmol.properties
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From: <ha...@us...> - 2026-01-01 02:53:57
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Revision: 22690
http://sourceforge.net/p/jmol/code/22690
Author: hansonr
Date: 2026-01-01 02:53:55 +0000 (Thu, 01 Jan 2026)
Log Message:
-----------
Jmol.___JmolVersion="16.3.43" // (legacy) also 16.3.44 (swingJS)
new feature: load filename FILL "UNITCELL_xxx"
-- key prefix "unitcell_" (case insensitive)
-- quotes are necessary
-- loads the filename (or "") using the unit cell information
included in the file itself. (as found in the model auxiliary
information _M as a key (lowercase) unitcell_xxx
new feature: (spin space groups) LOAD FILL "unitcell_x"
-- where x is L0, G0, magneticPrimitive, input
-- only preliminary tags at this point
new feature: MODELKIT SPACEGROUP >a,2b,c>
-- transform only, makes no attempt to change space group
-- works even for non-ITA groups, suchs as spin space groups
-- optional PACKED keyword
new feature: x = getProperty("cifinfo",cifdata)
-- adds CIF file data option
-- converts CIF data from a CIF file to map data
new feature: draw uc unitcell "1/2a,b,c" color white
-- draw a given unit cell
-- default ID is "uc"
-- default width is 3 pixels
-- default color is yellow
new feature: draw uc unitcell "1/2a,b,c" axes
-- draw a given unit cell, adding axis lines in red, green, and blue
-- default ID is "uc"
-- width for axes is slightly larger tha axes for clarity
-- default color is yellow
new feature: x = matrix("62.1>>62.5"), matrix("Pnma>>Pmcn")
-- returns Pp_abc transform for one setting to another
-- by ITA setting index or Hermann-Mauguin name
new feature: x = matrix("-b,-a,-c",TRUE)
-- normalizes to have center of the transformed unit cell
within the bounds of the abc unit cell
new feature: x = point([1 2 3])
-- point {1 2 3} from array [1 2 3]
new feature: DRAW DIAMETER n WIDTH x.x VECTOR ...
-- VECTOR with both DIAMETER int and WIDTH float
-- arrow head for vector is given the length of n * x.x
-- default (just WIDTH) is (unfortunately) just 0.5 A regardless of width
-- overrides defaultDrawArrowScale setting
new feature: select within(vxyz, @1)
-- selects the set of atoms with approximately the same spin as @1
-- matches vxyz within 0.01 precision
new feature: x = within("vxyz", @1)
-- returns set of atoms with approximately the same spin as @1
-- matches vxyz within 0.01 precision
new feature: select within(packing, unitcell)
-- selects the set of atoms within a fractional packing distance of the unit cell boundaries
-- negative value is that distance within the unit cell in all directions
new feature: x = within(packing, "unitcell")
-- returns the set of atoms within a fractional packing distance of 0.1 of the unit cell boundaries
-- negative value is that distance within the unit cell in all directions
new feature: x = within(packing, "unitcell", scale)
-- returns the set of atoms within a fractional packing distance of 0.1 of the unit cell boundaries
-- negative value is that distance within the unit cell in all directions
-- scales the unit cell by the given amount
new feature: x = within(packing, "unitcell", <unit cell description>)
-- where <unit cell description> is any value
-- negative value is that distance within the unit cell in all directions
-- for example:
new feature: x = within(packing, "unitcell", <unit cell description>, scale)
-- where <unit cell description> is any value
-- negative value is that distance within the unit cell in all directions
-- scales the unit cell by the given amount
new feature: x = unitcell("volume")
-- reports the current unit cell volume
-- also "a", "b", "c", "alpha", "beta", "gamma", "dim", "dimtype"
-- where "dim" reports 1, 2, or 3
-- and "dimtype" reports a number from 1 to 7 indicating
the periodic directions as three bits, cba
so 7 is abc periodic (space), 3 is ab periodic (plane or layer),
1 is periodic only along a (line or frieze)
new feature: x = unitcell(...,"info")
-- also just unitcell("info") for current model's unit cell
-- adding "info" as the final parameter for a unitcell() function
-- returns a map with keys:
isHexagonal
isRhombohedral
matCtoF
matFtoC
oabc
params
volume
where
matCtoF is the Cartesian-to-fractional matrix transform
matFtoC is the fractional-to-Cartesian matrix transform
oabc is the four-point array: [orgin, a, b, c]
params is a 15-element array that includes:
a,b,c,alpha,beta,gamma, // 1-6
va,vb,vc // 7-15
new feature: MODELKIT ... PACKED 0.x
-- MODELKIT ... PACKED ... commands can be followed by a range
-- extends this fraction beyond the unit cell edge
-- for example:
MODELKIT PACKED 0.1
MODELKIT UNITCELL PACKED 0.1 (same as MODELKIT PACKED 0.1)
MODELKIT UNITCELL {1 0 0} PACKED 0.1
MODELKIT ADD N {1/3 1/4 1/5} PACKED 0.2
bug fix: DRAW ... VECTOR
-- default width is 0.1 Angstroms (was 0.05 in 16.3.9/10)
bug fix: x = matrix("1/2a,1/b,c-0.12234","abc") fails
-- negative decimal fraction loses "-" sign
bug fix: render can sometimes flash lines when motion while calculations are being done
-- problem was with non-thread-safe rendering code for temp variables in TransformManager.java
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2025-12-13 18:45:26 UTC (rev 22689)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2026-01-01 02:53:55 UTC (rev 22690)
@@ -53,8 +53,140 @@
# FEATURE REQUEST: dock/undock consoles to main window.
# TODO: allow FIXED to work with MODELKIT MINIMIZE
-Jmol.___JmolVersion="16.3.41" // (legacy) also 16.3.42 (swingJS)
+Jmol.___JmolVersion="16.3.43" // (legacy) also 16.3.44 (swingJS)
+new feature: load filename FILL "UNITCELL_xxx"
+ -- key prefix "unitcell_" (case insensitive)
+ -- quotes are necessary
+ -- loads the filename (or "") using the unit cell information
+ included in the file itself. (as found in the model auxiliary
+ information _M as a key (lowercase) unitcell_xxx
+
+new feature: (spin space groups) LOAD FILL "unitcell_x"
+ -- where x is L0, G0, magneticPrimitive, input
+ -- only preliminary tags at this point
+
+new feature: MODELKIT SPACEGROUP >a,2b,c>
+ -- transform only, makes no attempt to change space group
+ -- works even for non-ITA groups, suchs as spin space groups
+ -- optional PACKED keyword
+
+new feature: x = getProperty("cifinfo",cifdata)
+ -- adds CIF file data option
+ -- converts CIF data from a CIF file to map data
+
+new feature: draw uc unitcell "1/2a,b,c" color white
+ -- draw a given unit cell
+ -- default ID is "uc"
+ -- default width is 3 pixels
+ -- default color is yellow
+
+new feature: draw uc unitcell "1/2a,b,c" axes
+ -- draw a given unit cell, adding axis lines in red, green, and blue
+ -- default ID is "uc"
+ -- width for axes is slightly larger tha axes for clarity
+ -- default color is yellow
+
+new feature: x = matrix("62.1>>62.5"), matrix("Pnma>>Pmcn")
+ -- returns Pp_abc transform for one setting to another
+ -- by ITA setting index or Hermann-Mauguin name
+
+new feature: x = matrix("-b,-a,-c",TRUE)
+ -- normalizes to have center of the transformed unit cell
+ within the bounds of the abc unit cell
+
+new feature: x = point([1 2 3])
+ -- point {1 2 3} from array [1 2 3]
+
+new feature: DRAW DIAMETER n WIDTH x.x VECTOR ...
+ -- VECTOR with both DIAMETER int and WIDTH float
+ -- arrow head for vector is given the length of n * x.x
+ -- default (just WIDTH) is (unfortunately) just 0.5 A regardless of width
+ -- overrides defaultDrawArrowScale setting
+
+new feature: select within(vxyz, @1)
+ -- selects the set of atoms with approximately the same spin as @1
+ -- matches vxyz within 0.01 precision
+
+new feature: x = within("vxyz", @1)
+ -- returns set of atoms with approximately the same spin as @1
+ -- matches vxyz within 0.01 precision
+
+new feature: select within(packing, unitcell)
+ -- selects the set of atoms within a fractional packing distance of the unit cell boundaries
+ -- negative value is that distance within the unit cell in all directions
+
+new feature: x = within(packing, "unitcell")
+ -- returns the set of atoms within a fractional packing distance of 0.1 of the unit cell boundaries
+ -- negative value is that distance within the unit cell in all directions
+
+new feature: x = within(packing, "unitcell", scale)
+ -- returns the set of atoms within a fractional packing distance of 0.1 of the unit cell boundaries
+ -- negative value is that distance within the unit cell in all directions
+ -- scales the unit cell by the given amount
+
+new feature: x = within(packing, "unitcell", <unit cell description>)
+ -- where <unit cell description> is any value
+ -- negative value is that distance within the unit cell in all directions
+ -- for example:
+
+new feature: x = within(packing, "unitcell", <unit cell description>, scale)
+ -- where <unit cell description> is any value
+ -- negative value is that distance within the unit cell in all directions
+ -- scales the unit cell by the given amount
+
+new feature: x = unitcell("volume")
+ -- reports the current unit cell volume
+ -- also "a", "b", "c", "alpha", "beta", "gamma", "dim", "dimtype"
+ -- where "dim" reports 1, 2, or 3
+ -- and "dimtype" reports a number from 1 to 7 indicating
+ the periodic directions as three bits, cba
+ so 7 is abc periodic (space), 3 is ab periodic (plane or layer),
+ 1 is periodic only along a (line or frieze)
+
+new feature: x = unitcell(...,"info")
+ -- also just unitcell("info") for current model's unit cell
+ -- adding "info" as the final parameter for a unitcell() function
+ -- returns a map with keys:
+
+ isHexagonal
+ isRhombohedral
+ matCtoF
+ matFtoC
+ oabc
+ params
+ volume
+
+ where
+
+ matCtoF is the Cartesian-to-fractional matrix transform
+ matFtoC is the fractional-to-Cartesian matrix transform
+ oabc is the four-point array: [orgin, a, b, c]
+ params is a 15-element array that includes:
+ a,b,c,alpha,beta,gamma, // 1-6
+ va,vb,vc // 7-15
+
+new feature: MODELKIT ... PACKED 0.x
+ -- MODELKIT ... PACKED ... commands can be followed by a range
+ -- extends this fraction beyond the unit cell edge
+ -- for example:
+ MODELKIT PACKED 0.1
+ MODELKIT UNITCELL PACKED 0.1 (same as MODELKIT PACKED 0.1)
+ MODELKIT UNITCELL {1 0 0} PACKED 0.1
+ MODELKIT ADD N {1/3 1/4 1/5} PACKED 0.2
+
+bug fix: DRAW ... VECTOR
+ -- default width is 0.1 Angstroms (was 0.05 in 16.3.9/10)
+
+bug fix: x = matrix("1/2a,1/b,c-0.12234","abc") fails
+ -- negative decimal fraction loses "-" sign
+
+bug fix: render can sometimes flash lines when motion while calculations are being done
+ -- problem was with non-thread-safe rendering code for temp variables in TransformManager.java
+
+
+JmolVersion="16.3.41" // (legacy) also 16.3.42 (swingJS)
+
new feature: spinCIF and FINDSPINGROUP output readers
-- work in collaboration with Bilbao Crystallographic Server (Bilbao, Spain)
and Southern University of Science and Technology (Shenzhen, China)
@@ -62,7 +194,7 @@
new feature: plot SPIN
-- displays the vectors of a magCIF or spinCIF file
- within a unit circle as a point group object
+ within a unit sphere as a point group object
new feature: plot SPIN POINTGROUP
-- displays the point group of the spin group
@@ -71,7 +203,7 @@
new feature: FRAME 1.1 1.2 SPLIT
-- places two specified models side-by-side in a "split-frame" configuration
- -- synchonizes rotation, as normal for frames
+ -- synchronizes rotation, as normal for frames
-- JmolDataFrames (PLOT and QUATERNION commands) do not zoom or translate, only rotate
-- allows echo in either frame using ECHO ID ... MODEL ... to associate the
text with its respective model
@@ -85,7 +217,7 @@
frame 1.1 2.1 split
(quaternion difference is a calculation of 4-dimensional helical "straightness"
- that has a direct correspondance with Ramachandron values.)
+ that has a direct correspondence with Ramachandron values.)
Rotating the quaternion unit sphere (on the right) until a cluster
is in front provides the view down the associated helix or beta pleated sheet
(on the left). The tighter the cluster, the more "straight" the helix is.
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