ps -- I failed to upload that last night -- it is there now. On Mon, Jun 15, 2015 at 2:42 AM, Robert Hanson <hans...@stolaf.edu> wrote:
> http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.15_2015.06.14b.zip > > testing appreciated -- I would like to release a new version of Jmol 14.2 > before the end of the week. > > Jmol.___JmolVersion="14.3.15_2015.06.13" > > bug fix: var firstPARAM = "p1_b"; x = [FIRSTParam: "p1_a"]; results in > lowering of case as [firstparam:....] > bug fix: set drawPicking draw;set drawpicking does not show handles > bug fix; point group not calculated when the selected atoms are a subset > of a model > bug fix: x.find("SMILES") is incorrect for structures that have > hypervalent atoms and branches such as inorganic nitrates > bug fix: msCIF reading with two models, and only one has displacement > modulation causes "render error" crash > bug fix: msCIF reader failing for Legendre polynomials of order greater > than 4 > bug fix: DRAW for quadrilateral broken when perspective depth is turned > off. > bug fix: SET ECHO IMAGE broken in JavaScript version > > > feature note: This version introduces several very powerful and very > different capabilities > to Jmol in the area of crystallograpy. Many of these > features are nonexistent > in other programs. They involve: > > - an extension of SMILES to compare bonding topology irrespective of > atom identity. > (Are these two atom environments both iscoahedral?) > > x = {@1 and 1.1 and connected(@1)}.find("SMILES", "*"} > y = {2.1}.find("SMARTS", x) > > - the generation of polyhedra in crystal structures for which only the > central atom > may be loaded. > (What is the atom environment around Au3 in this crystal structure?) > > load t.cif // just the unit cell, maybe just one atom even > polyhedra 4-12 UNITECELL @1 > > - the ability to load a given block of space (such as a > 10x10x10-Angstrom cube) > with a crystal structure irrespective of its given unit cell. > (Are these two structures that have totally different unit cells > really that different?) > > load t.cif FILL > load t.cif FILL 20 > load t.cif FILL {20 10 10} > load t.cif FILL [{0 0 0} {5.2 5.2 0} {-5.2 5.5 0} {1.3 0 3.3}] > > - the ability to show and draw the point group of a polyhedron > > load t.cif > polyhedron 12 unitcell @1 > select @1 > show pointgroup POLYHEDRON > draw pointgroup POLYHEDRON > > - the ability to extract information about polyhedra > > print getProperty("shapeInfo.polyhedra[1]").keys > > _ipt > center > modelIndex > planeCount > polygons > vertexCount > vertices > > - the ability to select polyhedra > > select polyhedra > select polyhedra(4) > > print polyhedra() > print polyhedra(4) > > > - the ability to draw points from derived arrays > > draw diameter 0.2 points > @{getProperty("shapeInfo.polyhedra[1].vertices")} > > > new feature: POLYHEDRA 12 UNITCELL > -- creates a polyhedron (12-gon in this case) around each of the > currerntly selected atoms that has that bonding environment > -- DOES NOT require atoms at these positions - can simply use the > unit cell and periodicity to find the relevant atom positions. > -- will check bonding as necessary using autobonding parameters > -- accepts all standard polyhedra options. For example: > > polyhedra 12,16 3.5 UNITCELL > > new feature: POLYHEDRA 4-16 > -- allows a range of unit cell bonding patterns. > -- in this case, same as 4,5,6,7,8,9,10,11,12,13,14,15,16 > > polyhedra 4-16 3.5 UNITCELL > > new feature: getProperty shapeInfo.polyhedra > > print getProperty("shapeInfo.polyhedra[1]").keys > > _ipt > center > modelIndex > planeCount > polygons > vertexCount > vertices > > new feature: draw POINTS [ array of points ] > > draw diameter 0.2 points > @{getProperty("shapeInfo.polyhedra[1].vertices")} > > new feature: show pointgroup POLYHEDRON > -- uses points from the polyhedron of the first selected atom > -- recommended to use specific atom reference in POLYHEDRA command: > > select @21 > polyhedron 3.5 UNITCELL > show pointgroup polyhedron > > > $ show pointgroup polyhedron > # 13 atoms > > > Oh Ci {2.1020985 -4.3122215 2.1430104} > > Oh nC4 3 2 > Oh C4_1 {0.99993926, -0.007795072, 0.0077921236} > Oh C4_2 {7.8514034E-7, -0.9997856, -0.020707628} > Oh C4_3 {7.619045E-7, 0.009661385, -0.9999533} > > Oh nC3 4 2 > Oh C3_1 {-0.58944535, 0.5712053, 0.57120806} > Oh C3_2 {-0.58944565, -0.5712049, -0.57120824} > Oh C3_3 {-0.5824926, -0.58349025, 0.5658989} > Oh C3_4 {0.5764604, -0.5864354, 0.5690228} > > Oh nC2 9 1 > Oh C2_1 {0.7004682, -0.71362424, -0.0092081865} > Oh C2_2 {0.7004673, 0.009209763, 0.7136251} > Oh C2_3 {0.99993926, -0.007795072, 0.0077921236} > Oh C2_4 {-0.70046806, -0.71362436, -0.009208187} > Oh C2_5 {-8.22445E-7, 0.7071046, -0.707109} > Oh C2_6 {7.8514034E-7, -0.9997856, -0.020707628} > Oh C2_7 {0.7056006, -0.019795598, -0.70833325} > Oh C2_8 {7.619045E-7, 0.009661385, -0.9999533} > Oh C2_9 {5.440252E-7, 0.70734024, 0.7068733} > > Oh nS6 4 2 > Oh S6_1 {-0.58944535, 0.5712053, 0.57120806} > Oh S6_2 {-0.58944565, -0.5712049, -0.57120824} > Oh S6_3 {-0.5824926, -0.58349025, 0.5658989} > Oh S6_4 {0.5764604, -0.5864354, 0.5690228} > > Oh nS4 2 2 > Oh S4_1 {0.99993926, -0.007795072, 0.0077921236} > Oh S4_2 {7.619045E-7, 0.009661385, -0.9999533} > > Oh nCs 9 1 > Oh Cs_1 {0.0, 0.7071068, -0.7071067} > Oh Cs_2 {0.0, -0.7071068, -0.7071068} > Oh Cs_3 {0.007949507, 0.020366998, -0.999761} > Oh Cs_4 {0.007952394, 0.999761, -0.020367} > Oh Cs_5 {1.0, 0.0, 0.0} > Oh Cs_6 {0.7030396, 0.014484465, 0.71100324} > Oh Cs_7 {0.7030395, 0.71100324, 0.014484464} > Oh Cs_8 {0.70023495, -0.008727634, -0.7138592} > Oh Cs_9 {0.7030395, -0.71100324, -0.014484464} > > Oh type nType nUnique > Oh E 1 1 > Oh Ci 1 1 > Oh Cs 9 9 > Oh Cn 16 23 > Oh Sn 6 12 > Oh TOTAL 46 > > > -- displays a table showing point group information. > -- notice that not all the operators may be found because of settings of > set pointGroupDistanceFactor 0.2 being too tight a restriction. > > new feature: draw POINTS <list of points or array of points> > new feature: draw POLYGON <list of points or array of points> -1 > -- these two are identical; POINTS is a bit nicer. > > load "file:/C:/temp/aflow/binary/AgCd.aflow_binary" 20 //filter > "ca=0.5;nopack" > > select @1 & 1.1 > polyhedra 4-16 3.7 unitcell > > x = within(4, true, "unitcell", {selected}) > print x; > > draw width 0.2 points @{x["points"]} color red mesh nofill translucent > > > new feature: select POLYHEDRA > -- selects central atoms of any atoms having polyhedra. > > new feature: select polyhedra(4) > -- selects central atoms of any atoms having tetrahedral polyhedra. > > new feature: x.find("SMILES","*") > -- creates a topology SMILES, involving just * and connections > -- does not include stereochemistry > -- allows comparison of connection patterns without respect to any other > consideration. > -- can be used to check equivalences in inorganic crystal structures. > > > code: SMILES code cleaned up. > code: most image loading is now asynchronous. (Not BMP, not from PNGJ > files with "|" in filename) > code: introducing interfaces to allow less use of @j2sNative and more > traceability of method calls in Eclipse > > > > bug fix: polyhedra broken for number of vertices > 6. > -- needed smaller default distanceFactor (set to 1.5; formerly 1.85) > -- this setting is for any > > > > > -- > 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 > > -- 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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