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From: Robert H. <ha...@st...> - 2024-03-19 07:12:17
|
Sorry for the delay. This is fixed. I'll get this in the next release, hopefully later today or tomorrow. |
From: Robert H. <ha...@st...> - 2024-03-19 04:50:28
|
for reference, it was missing this line: CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 |
From: Robert H. <ha...@st...> - 2024-03-19 04:49:58
|
Thanks, Eric. I will check that out. Actually, I see a problem with that file also. Jmol/SwingJS (JavaD.jar, 16.2.2, on the left) is reading more than Jmol 16.2.1 (on the right): [image: image.png] But the particular issue you are referring to is due to the fact that there is no symmetry information in that file, yet it refers to biomolecules. [image: image.png] On Sat, Mar 16, 2024 at 12:08 PM m0lviz--- via Jmol-users < jmo...@li...> wrote: > Dear Bob, > > The following load command > > load model ({0}) " > http://bioinformatics.org/molvis/tmp/consurf/dimer_with_symmetry_header.pdb" > filter "!_H;*.CA;*.P;%A;ALLHET;biomolecule 1;bmchains;/=3" > > fails in 16.1.53 and later releases including 16.2.1. > However it works in 16.1.47 and earlier releases. > (I did not test releases 48-52). > > This filter is standard in FirstGlance for large assemblies such as virus > capsids. *It works with published PDB files having a complete header > section*. For example this works in 16.2.1: > > load MODELS ({0}) https://files.rcsb.org/download/7R1C.pdb filter > "!_H;*.CA;*.P;%A;ALLHET;biomolecule 3;bmchains;/=3"; > spacefill; > > I suspect that the bug derives from dimer_with_symmetry_header.pdb *lacking > a complete header section*. It has a minimal header, just sufficient for > FirstGlance to process its REMARK 350 symmetry operations to generate the > biomolecule (see > https://bioinformatics.org/firstglance/fgij4.2/notes.htm#dotpdb ). > > Incidentally, when the command fails in JSmol (in FirstGlance) in Firefox, > even after closing the browser tab in which the failure occurred, clicking > links in Firefox fails until Firefox is quit and re-started. > > Because the current public release of FirstGlance (version 4.1) uses JSmol > 14.32.69 lacking the bug in question, you can see the desired result in > FirstGlance with this link: > > > https://proteopedia.org/wiki/fgij/fg.htm?mol=http://bioinformatics.org/molvis/tmp/consurf/dimer_with_symmetry_header.pdb&bu=1&aunonh=5086&aubb=648&bu2auquotient=110.0000 > > (This link is automatically generated when you > > 1. Paste into the "molecule's URL" slot of FirstGlance > http://bioinformatics.org/molvis/tmp/consurf/dimer_with_symmetry_header.pdb > 2. Click on "Functional Assemblies". > 3. Click on "220 chains".) > > > -Eric > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- 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 *We stand on the homelands of the Wahpekute Band of the Dakota Nation. We honor with gratitude the people who have stewarded the land throughout the generations and their ongoing contributions to this region. We acknowledge the ongoing injustices that we have committed against the Dakota Nation, and we wish to interrupt this legacy, beginning with acts of healing and honest storytelling about this place.* |
From: Robert H. <ha...@st...> - 2024-03-19 01:32:29
|
Pat, I would love to get more SHELX functionality working. Can you help? Bob |
From: Carroll, P. J <car...@sa...> - 2024-03-18 23:54:39
|
Norwid, "Show Q peaks" is "select Q*; cpk 10%; wireframe 0; color limegreen; label %a; color labels limegreen; set labelOffset {0, 1.1, 0}" "No Q-peaks" is "select Q*; cpk 0; labels OFF" And, yes, I messed up with the red-green glasses! It should be red-blue glasses! When you make a bazillion variations, an incorrect one can become immortal - at some point, I must have had red-green glasses! Pat ________________________________________ From: Norwid Behrnd via Jmol-users <jmo...@li...> Sent: Monday, March 18, 2024 5:44 PM To: jmo...@li... Cc: Norwid Behrnd Subject: Re: [Jmol-users] Jmol 16.2.1 - major upgrade for crystallography education Dear Pat, aiming to replicate your implementation, I accessed the JSmol console of the web page indicated by you. The toggle on the q peaks on your page seems to run by ``` select Q*; cpk 0; labels off ``` It doesn't seem to be the whole recipe though because in a local test, for me (Jmol 16.2.1 by 2024-03-15) the most similar result is obtained with ``` select Q*, color green; labels off ``` A really nice additional feature of your site is the optional output as an anaglyph. Note, instead of the red-green goggles announced, the call of `background lightgrey; stereo REDBLUE` seems to use a slightly different model.[1] Norwid [1] https://urldefense.com/v3/__https://chemapps.stolaf.edu/jmol/docs/index.htm?command=stereo&ver=16.2__;!!IBzWLUs!WKXWK0W-G24ZlGVqZ8Gh-aeI3j1jf-FOPr_oV4H18sJCVn7-1tVfowWo2wS4fLTIZSqsocYd8TX1ZiQjBuiQn8OiNTtgvQpk$ _______________________________________________ Jmol-users mailing list Jmo...@li... https://urldefense.com/v3/__https://lists.sourceforge.net/lists/listinfo/jmol-users__;!!IBzWLUs!WKXWK0W-G24ZlGVqZ8Gh-aeI3j1jf-FOPr_oV4H18sJCVn7-1tVfowWo2wS4fLTIZSqsocYd8TX1ZiQjBuiQn8OiNbnpINQM$ |
From: Norwid B. <nb...@ya...> - 2024-03-18 21:55:35
|
Dear Pat, aiming to replicate your implementation, I accessed the JSmol console of the web page indicated by you. The toggle on the q peaks on your page seems to run by ``` select Q*; cpk 0; labels off ``` It doesn't seem to be the whole recipe though because in a local test, for me (Jmol 16.2.1 by 2024-03-15) the most similar result is obtained with ``` select Q*, color green; labels off ``` A really nice additional feature of your site is the optional output as an anaglyph. Note, instead of the red-green goggles announced, the call of `background lightgrey; stereo REDBLUE` seems to use a slightly different model.[1] Norwid [1] https://chemapps.stolaf.edu/jmol/docs/index.htm?command=stereo&ver=16.2 |
From: Carroll, P. J <car...@sa...> - 2024-03-18 18:52:07
|
Bob and Norwid, Decided it's just as easy to handle the Q-peaks with scripts: http://crystal.chem.upenn.edu/aca09/1479.html Pat ________________________________________ From: Carroll, Patrick J <car...@sa...> Sent: Saturday, March 16, 2024 5:42 PM To: jmo...@li... Subject: Re: [Jmol-users] Jmol 16.2.1 - major upgrade for crystallography education Norwid, Yes, that would be good also. Maybe also an ON/OFF command like for hydrogens. (Making more work for progammers!) Pat Sent from my iPhone while enjoying a very dry martini > On Mar 16, 2024, at 5:25 PM, Norwid Behrnd via Jmol-users <jmo...@li...> wrote: > > Dear Pat, > > regarding Jmol's processing of .res files, wouldn't it be nicer if the q > peak's color assigned by default were different to the one about carbon atoms, > too? Influenced by the approach in Olex2, for instance with a representation > with semi-transparent gold, instead of opaque black/gray? As an illustration > for Bob, I enclose a public screen photo about sucrose.[1] > > Norwid > > [1] https://urldefense.com/v3/__http://verahill.blogspot.com/2013/06/462-olex2-11-on-debian.html__;!!IBzWLUs!U4VGD9uu_3Gg_qw15_gamg5rWitSRIbI7JJx10CM8CnXw4QEj1zyy-55V7FLdbkTI-uJRH48HMscTubtfnPfmJQT1qPpyr9R$ > <olex2.png> > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://urldefense.com/v3/__https://lists.sourceforge.net/lists/listinfo/jmol-users__;!!IBzWLUs!U4VGD9uu_3Gg_qw15_gamg5rWitSRIbI7JJx10CM8CnXw4QEj1zyy-55V7FLdbkTI-uJRH48HMscTubtfnPfmJQT1hFv_zjT$ _______________________________________________ Jmol-users mailing list Jmo...@li... https://urldefense.com/v3/__https://lists.sourceforge.net/lists/listinfo/jmol-users__;!!IBzWLUs!VkMb--KC6ZYKCocbQfE03NOa4Vwgam7i1npG7eO8mqvksdgm_L7oYHTeGCnheAe6rCBO5F0lk6HWpSa68X8pNczitg$ |
From: Carroll, P. J <car...@sa...> - 2024-03-16 21:58:01
|
Norwid, Yes, that would be good also. Maybe also an ON/OFF command like for hydrogens. (Making more work for progammers!) Pat Sent from my iPhone while enjoying a very dry martini > On Mar 16, 2024, at 5:25 PM, Norwid Behrnd via Jmol-users <jmo...@li...> wrote: > > Dear Pat, > > regarding Jmol's processing of .res files, wouldn't it be nicer if the q > peak's color assigned by default were different to the one about carbon atoms, > too? Influenced by the approach in Olex2, for instance with a representation > with semi-transparent gold, instead of opaque black/gray? As an illustration > for Bob, I enclose a public screen photo about sucrose.[1] > > Norwid > > [1] https://urldefense.com/v3/__http://verahill.blogspot.com/2013/06/462-olex2-11-on-debian.html__;!!IBzWLUs!U4VGD9uu_3Gg_qw15_gamg5rWitSRIbI7JJx10CM8CnXw4QEj1zyy-55V7FLdbkTI-uJRH48HMscTubtfnPfmJQT1qPpyr9R$ > <olex2.png> > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://urldefense.com/v3/__https://lists.sourceforge.net/lists/listinfo/jmol-users__;!!IBzWLUs!U4VGD9uu_3Gg_qw15_gamg5rWitSRIbI7JJx10CM8CnXw4QEj1zyy-55V7FLdbkTI-uJRH48HMscTubtfnPfmJQT1hFv_zjT$ |
From: Norwid B. <nb...@ya...> - 2024-03-16 21:25:11
|
Dear Pat, regarding Jmol's processing of .res files, wouldn't it be nicer if the q peak's color assigned by default were different to the one about carbon atoms, too? Influenced by the approach in Olex2, for instance with a representation with semi-transparent gold, instead of opaque black/gray? As an illustration for Bob, I enclose a public screen photo about sucrose.[1] Norwid [1] http://verahill.blogspot.com/2013/06/462-olex2-11-on-debian.html |
From: Carroll, P. J <car...@sa...> - 2024-03-16 20:37:35
|
Bob, I was excited to see all the crystallography gadgets you've added to Jmol and am eager to try them out. But it appears that the recent versions of Jmol (v. 16 +) do not correctly interpret the symmetry positions written in the SHELX type .res files. These ".res" files are very important because they are the result files from the SHELXL refinement program, which is used in most crystallographic refinements. Any of the res files I've tried report the space group as P1, i.e, a space group that has no symmetry operations (the cell includes only the primary position at x, y, z). As an example, see this link: http://crystal.chem.upenn.edu/aca09/1479_TEST.html which displays a molecule in space group P2(1), which should have two symmetry positions: x, y, z and -x, 0.5+y, -z. In addition, it would be nice if Jmol didn't display the so-called "Q-peaks." These peaks are listed at the end of the .res file and are the residual peaks in the final electron density map. Pat Carroll U Penn (ret.) ________________________________________ From: Robert Hanson via Jmol-users <jmo...@li...> Sent: Friday, March 15, 2024 10:27 PM To: jmo...@li... Cc: Robert Hanson Subject: [Jmol-users] Jmol 16.2.1 - major upgrade for crystallography education Dear Jmol users, Jmol-16.2.1-binary.zip (63.3 MB)<https://urldefense.com/v3/__https://sourceforge.net/projects/jmol/files/latest/download__;!!IBzWLUs!X4ra2beEGVmgD_fL7nSLT9GpXUWiz3yFw9uSOKsgO3eTMcP_dQC3mvYLyKjctZ0oRwAemaiHq-6XsbLPKGY1tYbau_EP9ASb$> Moving to a new version set (16.2.x) signals a major update, primarily relating to crystallographic symmetry. This message contains a list of all the new features since 15.2 (15 months ago, about 160). A lot has been added! We basically have a fully functional crystal building capability. This is thanks in no small way to the financial support and enthusiasm provided by the developers of Q-Studio<https://urldefense.com/v3/__https://qs.pwmat.com__;!!IBzWLUs!X4ra2beEGVmgD_fL7nSLT9GpXUWiz3yFw9uSOKsgO3eTMcP_dQC3mvYLyKjctZ0oRwAemaiHq-6XsbLPKGY1tYbauyJNomiI$>, a web app specifically geared toward crystal structure building for computational crystallography. The team there has done a fantastic job of building a context around JSmol that makes designing and building crystal structures a snap. Thank you, team! In addition, I want to thank the team at the Bilbao Crystallographic Server<https://urldefense.com/v3/__https://www.cryst.ehu.es__;!!IBzWLUs!X4ra2beEGVmgD_fL7nSLT9GpXUWiz3yFw9uSOKsgO3eTMcP_dQC3mvYLyKjctZ0oRwAemaiHq-6XsbLPKGY1tYbau0VitaXU$> for hosting me in Bilbao and patiently guiding me through the process of understanding the nuances of space groups and the mathematics of crystallography. This was critical. So great to work with you! I don't doubt that there are a few bugs here. It was a very complex task getting all the crystal structure building and space group loading and switching working. I encourage those with an interest in teaching about crystallographic symmetry to give some of this a try. I'm already finding it quite enticing, and I think you will, too. I don't think there's ever been a platform like this that allows the creative design of powerful, interactive visualizations of this sort. (Publication forthcoming!) The sooner we can find the bugs, the sooner we can get them taken care of. I include here a model of space group 20 and one of its subgroups (ITA 4), with both unit cells indicated, aligned, and packed. You can see that there is a two-fold screw axis common to both; the rest of the symmetry of group 20 has been lost in going to space group 4. The "atoms" are all related to one general position site of space group 20, which has a multiplicity of 8 and were added using the simple command, modelkit add P wyckoff G. They are colored based on their site (color property site) for space group 4, where the eight-coordinate general position orbit of space group 20 has been split into four pairs of equivalent atoms in space group 4. The additional four atoms in uc-4 fill out the packing of that unit cell. The information needed to create this image, from https://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-tranmax?way=up&super=20&sub=4&index=2&client=maxsub&what=&path=&series=&conj=all&type=t<https://urldefense.com/v3/__https://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-tranmax?way=up&super=20&sub=4&index=2&client=maxsub&what=&path=&series=&conj=all&type=t__;!!IBzWLUs!X4ra2beEGVmgD_fL7nSLT9GpXUWiz3yFw9uSOKsgO3eTMcP_dQC3mvYLyKjctZ0oRwAemaiHq-6XsbLPKGY1tYbau0SyJEbb$> is just the two space group numbers and the unit cell transformation, which in this case is [1/2a+1/2b,c,1/2a-1/2b ; 0,0,0]. The short script used to create this image is WAY down at the bottom of this page. You might be surprised how few lines of script were needed to create this model. Of course, this is a PNGJ file. Enjoy! [g20-sg4-w-4-draw-sg-packed.png] I know I am WAY behind on interactive documentation. (Volunteers welcome!!!) Everything I do, though, is described in https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/viewer/Jmol.properties<https://urldefense.com/v3/__https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/viewer/Jmol.properties__;!!IBzWLUs!X4ra2beEGVmgD_fL7nSLT9GpXUWiz3yFw9uSOKsgO3eTMcP_dQC3mvYLyKjctZ0oRwAemaiHq-6XsbLPKGY1tYbau8_VjK8z$> Bob Hanson ----------------------------------------------------------------------------------- Jmol.___JmolVersion="16.2.1" // (legacy) also 16.2.2 (swingJS) bug fix: when unit cells are modified, Symmetry should not be assumed to be unchanged. bug fix: unit cell information should only show space group if symmetry if the unit cell is appropriate bug fix: with set picking SYMMETRY, double-clicks should not start measurements bug fix: LOAD SUPERCELL should retain symmetry-relatad cell as "conventional" new feature: "contrast" color -- for LABEL and ECHO, particularly -- chooses WHITE or BLACK, depending upon the Jmol window background color -- saved in the state as [xfedcba] new feature: set picking SYMMETRY now aliased with set picking SYMOP new feature: MODELKIT SPACEGROUP "HALL:xx xx xx" will create a space group from a Hall or extended Hall description -- future enhancement will allow any HALL description -- see "Space-group notation with an explicit origin", S. R. Hall, Acta Cryst. (1981). A37, 517-525 https://doi.org/10.1107/S0567739481001228<https://urldefense.com/v3/__https://doi.org/10.1107/S0567739481001228__;!!IBzWLUs!X4ra2beEGVmgD_fL7nSLT9GpXUWiz3yFw9uSOKsgO3eTMcP_dQC3mvYLyKjctZ0oRwAemaiHq-6XsbLPKGY1tYbau9G5Z1rL$> http://macxray.chem.upenn.edu/LATT.pdf thank you, Patrick Carroll http://cci.lbl.gov/sginfo/hall_symbols.html<https://urldefense.com/v3/__http://cci.lbl.gov/sginfo/hall_symbols.html__;!!IBzWLUs!X4ra2beEGVmgD_fL7nSLT9GpXUWiz3yFw9uSOKsgO3eTMcP_dQC3mvYLyKjctZ0oRwAemaiHq-6XsbLPKGY1tYbau0YxKhd5$> http://cci.lbl.gov/cctbx/explore_symmetry.html<https://urldefense.com/v3/__http://cci.lbl.gov/cctbx/explore_symmetry.html__;!!IBzWLUs!X4ra2beEGVmgD_fL7nSLT9GpXUWiz3yFw9uSOKsgO3eTMcP_dQC3mvYLyKjctZ0oRwAemaiHq-6XsbLPKGY1tYbau7FDPsQb$> new feature: MODELKIT SPACEGROUP ... UNITCELL [a b c alpha beta gamma] PACKED -- after ZAP, creates a new space group with the given unit cell -- optionally packing it, if not after ZAP -- if the unit cell is incompatible with the space group, a similar compatible cell is used version: Version 16.2 represents a major advance in capability for Jmol, particularly in the area of space groups and symmetry in relation to 16.1.1, released 2023.01.24. The following is the listing of 90 new features since then, culled from this file and sorted. More detail on these can be found below. new feature: CONFIGURATION -n new feature: CONFIGURATION "A" new feature: "contrast" color new feature: crystal structure set picking dragMolecule with ALT implemented new feature: DRAW "<hover>xxx</hover>...." new feature: DRAW boundbox $[isosurface id] new feature: DRAW boundbox BEST $[isosurface id] new feature: DRAW HOVERLABEL "xxx" new feature: DRAW SPACEGROUP @a n new feature: DRAW SPACEGROUP @n new feature: DRAW SPACEGROUP ALL new feature: DRAW SYMOP [3,4,5] @1 new feature: ECHO/DRAW with ID starting with "_!_" new feature: Jmol application -A --scriptarguments flag new feature: LOAD "$?" load structure from NCI/CADD with prompt new feature: LOAD "*?" load PDB ID from EBI with prompt new feature: LOAD ":?" load structure from pubChem with prompt new feature: LOAD "=?" load PDB ID from RCSB with prompt new feature: LOAD "==?" load chemical component from RCSB with prompt new feature: LOAD .... fill "rhombohedral" new feature: LOAD .... fill "trigonal" new feature: LOAD =aflowlib/155.2 new feature: LOAD...FILTER "lowPrecision" new feature: LOAD...FILTER "PRECISION=n" where n is up to 16 digits new feature: LOAD - allow CIFReader to ignore COD 2107628 unmodulated operations in presence of modulated new feature: LOAD - AMS reader new feature: LOAD - BilbaoReader allows LOAD ... spacegroup ":n" to force origin, where n is 1 or 2 new feature: LOAD - Binary CIF file structure reading. The BinaryCIF file format new feature: LOAD - CIFReader "ignoreGeomBond" (was SwingJS only) new feature: LOAD - CIFReader FILTER option NOWYCKOFF new feature: LOAD - CIFReader reads atom_site_wyckoff_label new feature: LOAD - CrystalMaker CMDF (binary) file reader new feature: LOAD - Jmol will accept CIF files with duplicate atom_site_label entries new feature: MACRO AFLOW adds SHOWSG(n,i,addSymmetry) new feature: MEASURE .... "default" new feature: MEASURE SELECT ALL new feature: MEASURE SELECT... new feature: MEASURE SELECTED new feature: MEASURE SELECTED ... new feature: MINIMIZE GROUP {atoms} new feature: MINIMIZE ONLY {atoms} new feature: MINIMIZE SELECT {atoms} new feature: MODELKIT ADD <elem> WYCKOFF <Aa-z> new feature: MODELKIT MINIMIZE new feature: MODELKIT MOVETO @atoms @points new feature: MODELKIT SET KEY ON/OFF new feature: MODELKIT SPACEGROUP "HALL:xxxxx" will create a space group from a Hall or extended Hall description new feature: MODELKIT SPACEGROUP "x,y,z;x,-y,z;..." new feature: MODELKIT SPACEGROUP ... UNITCELL ... new feature: MODELKIT VIBRATION WYCKOFF; VIBRATION ON new feature: POLYHEDRA OFFSET {x, y, z} WIGNERSEITZ new feature: POLYHEDRA OFFSET 1.0 BRILLOUIN n where n > 1 new feature: POLYHEDRON LIST new feature: popup menu adds "atom picking..." Drag Atom and Drag Molecule new feature: RESTORE UNITCELL name new feature: SAVE UNITCELL name new feature: SELECT CONFIG=0 new feature: SET minimizationReportSteps new feature: SET picking DRAGMOLECULE for crystal structures new feature: SET picking SYMMETRY now aliased with set picking SYMOP new feature: SET symmetryHM TRUE new feature: SMILES/ALLCOMPONENTS flag for generation of SMILES having multiple components new feature: threaded symmetry-aware UFF minimization of crystal structures. new feature: UFF minimization with application of symmetry for new feature: UNITCELL [a,b,c,alpha,beta,gamma] new feature: UNITCELL RHOMBOHEDRAL and UNITCELL TRIGONAL (or HEXAGONAL - same) new feature: ZAP;MODELKIT SPACEGROUP ... UNITCELL [a b c alpha beta gamma] PACKED new feature: x = (array of SMILES strings).find("SMARTS" or "SMILES", pattern) new feature: x = _args() and _args(n) new feature: x = _arguments and _argumentCount added to SET CALLBACK "jmolscript:..." new feature: x = {*}.find("spacegroup", "parent") new feature: x = {atomset}.atoms and {atomset}.label("%[atoms]") new feature: x = 3x3matrix%1 new feature: x = 3x3matrix%2 new feature: x = atomset.search(pat) new feature: x = compare(A, B, map) and compare(A, B, map, "stddev") new feature: x = function special variables _caller, _callers, _name new feature: x = pattern(<smarts string>) new feature: x = search(target, pattern) new feature: x = spacegroup("ITA/155.1") new feature: x = spacegroup("ITA/ALL") new feature: x = symop("count") new feature: x = symop(matrix,option) new feature: x = symop("wyckoff") new feature: x = symop("wyckoff", "c") new feature: x = symop("wyckoff","C") new feature: x = symop("wyckoff","G") new feature: x = symop("wyckoff","S") new feature: x = @@3.symop("wyckoff",option) new feature: x = {atom}.wyckoff, label %[wyckoff], color PROPERTY WYCKOFF new feature: x = string.pop() new feature: x = string.push("xx") This extends the initial set of 85 new crystallographic features introduced in version 15.2: new feature: CALCULATE POINTGROUP {atoms} new feature: CALCULATE SPACEGROUP new feature: CALCULATE SPACEGROUP {atoms} new feature: CENTER UNITCELL new feature: DRAW HKL {1 1 1 x.x} new feature: DRAW HKL {1 1 1} OFFSET x.x new feature: DRAW INTERCEPT UNITCELL xxx LATTICE {na nb nc}... HKL .... new feature: DRAW intersection [unitcell or boundbox description] [line or plane description] new feature: DRAW intersection [unitcell or boundbox description] LINE @1 @2 new feature: DRAW intersection [unitcell or boundbox description] ON [line or plane description] new feature: DRAW POINTGROUP {atoms} CENTER xx new feature: DRAW UNITCELL xxx LATTICE {na nb nc} new feature: GETPROPERTY unitCellInfo new feature: ISOSURFACE SLAB designations "a=" "b=" "c=" "-a=" "-b=" "-c=" "ab" "bc" "ac" "-ab" "-bc" "-ac" new feature: LOAD .... SPACEGROUP "Hall:P 2y" new feature: LOAD [some crystal structure] filter "POLYMERX" new feature: LOAD [some crystal structure] filter "SLABXY" new feature: LOAD spacegroup 213 unitcell [5 5 5 90 90 90] new feature: LOAD xxxx.mol FILTER "no3D" new feature: LOAD xxxx.mol FILTER "noHydrogen" (Or just "NOH") new feature: MINIMIZE now works (minimally) with a crystal structure. new feature: MODELKIT ON/OFF new feature: MODELKIT ADD "C" point [PACKED] new feature: MODELKIT ADD "Cl" {1/2 1/3 1/3} new feature: MODELKIT ADD "Cl" {1/2 1/3 1/3} PACKED new feature: MODELKIT ADD @1 new feature: MODELKIT ADD @1 "Cl" {1/2 1/3 1/3} new feature: MODELKIT ADD @1 "Cl" {1/2 1/3 1/3} PACKED new feature: MODELKIT ADD @1 "N" new feature: MODELKIT ADD @1 "N" PACKED new feature: MODELKIT ADD @1 PACKED new feature: MODELKIT ADD @2 "C" [PACKED] new feature: MODELKIT ADD @2 [PACKED] new feature: MODELKIT ADD {xxx} PACKED new feature: MODELKIT ADD C [array of points] new feature: MODELKIT ADD/DELETE/MOVETO new feature: MODELKIT CONNECT @1 @2 [0,1,2,3,4,5,p,m] (default 1) new feature: MODELKIT DELETE {atoms} new feature: MODELKIT FIXED NONE new feature: MODELKIT FIXED PLANE plane new feature: MODELKIT FIXED VECTOR point1 point2 new feature: MODELKIT MOVETO @1 {1/2 0 0} new feature: MODELKIT MUTATE new feature: MODELKIT PACKED new feature: MODELKIT ROTATE axis1 axis2 {atoms} degrees new feature: MODELKIT SET autobond true new feature: MODELKIT SET hidden true new feature: MODELKIT SPACEGROUP new feature: MODELKIT SPACEGROUP "P1" new feature: MODELKIT SPACEGROUP 123 new feature: MODELKIT SPACEGROUP 123 packed new feature: MODELKIT SPACEGROUP ... UNITCELL [a b c alpha beta gamma] PACKED new feature: MODELKIT SPACEGROUP "ITA/itno.setting" (e.g. "ITA/155.2") new feature: MODELKIT SPACEGROUP "HALL:xx xx xx" new feature: MODELKIT UNDO/REDO new feature: MODELKIT UNITCELL [unitcell description] new feature: ModelKitCallback new feature: MOVETO AXES [-][ab, bc, ca, ba, cb, ac][1, 2, 3, 4] new feature: plane designations "ab" "ab1" "ac "ac1" "bc" bc1" short for {0 0 1/1 0} {0 0 1/1 c} etc. new feature: set picking dragAtom TRUE now recognizes symmetry for crystal structures new feature: UNITCELL FILL {na nb nc} new feature: UNITCELL OFFSET @1; UNITCELL OFFSET {atoms} new feature: UNITCELL SUPERCELL {na nb nc} new feature: UNITCELL SURFACE {h k l} [height | scale%] [offset or offset%] [TOP] new feature: x = @@1.symop(2, "invariant") new feature: x = @1.pointgroup("spacegroup") new feature: x = @1.symop("invariant") new feature: x = [{point},{point},...].find("equivalent", flags) { new feature: x = {*}.find("spacegroup") -- discovers the space group for a model new feature: x = {*}.find("spacegroup","x,y,-z") new feature: x = {*}.inchi("fixedh?") new feature: x = {*}.inchi("standard") new feature: x = {1/2 1/2 1/2}.symop("invariant") new feature: x = {1/2 1/2 1/2}.symop(2, "invariant") new feature: x = {atoms}.pointGroup() new feature: x = hkl(1 0 0 0.3) to produce plane offset by 0.3 Angstroms from the origin. new feature: x = load(filename, asbinary, async) or load(filename, nbytesMax, async) or load(filename, "JSON", async) new feature: x = search(atomset) new feature: x = spacegroup("123") or spacegroup(123) new feature: x = spacegroup("x,y,z&-x,y,z") or spacegroup("&x,y,z;-x,y,z") or spacegroup("x,y,z;-x,y,z&") new feature: x = spacegroup("x,y,z;-x,y,z") new feature: x = spacegroup("x,y,z;-x,y,z", [a, b, c, alpha, beta, gamma]) new feature: x = spacegroup(6, [a, b, c, alpha, beta, gamma]) new feature: x = symop(2, "invariant") new feature: x = symop(3,@1,"array") adds "xyzNormalized" new feature: ZOOM UNITCELL 0 new feature: ZOOMTO UNITCELL 0 bug fix: changing unit cell using just UNITCELL rather than MODELKIT UNITCELL improperly retains symmetry -- when the unit cell is offset, symmetry should drop to P1 -- when the unit cell is RESET or otherwise returned to the one associated with the space group, symmetry should be returned bug fix: unit cell information displayed should represent the space group accurately -- file-based symmetry initially should reflect the operators from the file -- after MODELKIT SPACEGROUP, the information should reflect a specific setting in Jmol and ITA, if found. new feature: MODELKIT SPACEGROUP ... UNITCELL ... -- adds the ability to set the space group and unit cell at the same time -- unit cell parameters must be compatible with the space group, or the action is aborted -- unit cell can be expressed in one of three formats: -- as the array [a b c alpha beta gamma] -- as the array of cartesian vectors [origin, va, vb, vc} -- as the setting transformation string "a,b,c;0,0,0" new feature: set symmetryHM TRUE -- for show/calculate/draw POINTGROUP -- TRUE switches to Hermann-Mauguin (2m, 2/m2/m2/m) notation -- FALSE switches back to the default Schoenflies (C2v, D2h) notation example script: -- creating a group-subgroup comparison, where the transform between settings is known -- based on information at https://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-tranmax?way=up&super=20&sub=4&index=2&client=maxsub&what=&path=&series=&conj=all&type=t<https://urldefense.com/v3/__https://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-tranmax?way=up&super=20&sub=4&index=2&client=maxsub&what=&path=&series=&conj=all&type=t__;!!IBzWLUs!X4ra2beEGVmgD_fL7nSLT9GpXUWiz3yFw9uSOKsgO3eTMcP_dQC3mvYLyKjctZ0oRwAemaiHq-6XsbLPKGY1tYbau0SyJEbb$> zap modelkit spacegroup 20 draw u20 unitcell color orange mesh nofill "uc-20" modelkit add P Wyckoff G // switching to sg 4 -- note that the listed transform matrix // is for subgroup to supergroup; we need the opposite here, thus the "!" prefix modelkit spacegroup 4 unitcell "!1/2a+1/2b,c,1/2a-1/2b" // drawing unit cell and operations draw uc4 unitcell diameter 0.01 color orange mesh nofill "uc-4" color property site draw id "s12" symop @1 @2 draw id "s43" symop @4 @3 draw id "s56" symop @5 @6 draw id "s87" symop @8 @7 draw id "sg4" spacegroup all //write c:\\temp\\iucr\\g20-sg4-w-4-draw.png as PNGJ // switching back to sg 20: modelkit spacegroup 20 unitcell "1/2a+1/2b,c,1/2a-1/2b" print symop("wyckoff") print {*}.wyckoff.pivot; // switching to sg 4: modelkit spacegroup 4 unitcell "!1/2a+1/2b,c,1/2a-1/2b" print symop("wyckoff") print {*}.wyckoff.pivot; -- Robert M. Hanson Professor of Chemistry, Emeritus St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr<https://urldefense.com/v3/__http://www.stolaf.edu/people/hansonr__;!!IBzWLUs!X4ra2beEGVmgD_fL7nSLT9GpXUWiz3yFw9uSOKsgO3eTMcP_dQC3mvYLyKjctZ0oRwAemaiHq-6XsbLPKGY1tYbau8ZYAuBC$> 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 We stand on the homelands of the Wahpekute Band of the Dakota Nation. We honor with gratitude the people who have stewarded the land throughout the generations and their ongoing contributions to this region. We acknowledge the ongoing injustices that we have committed against the Dakota Nation, and we wish to interrupt this legacy, beginning with acts of healing and honest storytelling about this place. |
From: Andrei I. A. <and...@ya...> - 2024-03-16 18:05:09
|
Dear, I'm writing you again about a bug with the JSpecView. I'm trying to load the example 'jsv.htm' file on an web server and I got an error: --Uncaught TypeError: Cannot read properties of undefined (reading 'indexOf') at Function.eval [as getQuotedAttribute] (corejsv.z.js:446:69) at Object.eval [as construct] (corejsv.z.js:1002:318) at a.instantialize (JSmol.min.js:197:17) at new eval (corejsv.z.js:1002:221) at eval (corejsv.z.js:1008:452) at updateNode (JSmol.min.js:247:371) at updateNode (JSmol.min.js:249:274) at updateNode (JSmol.min.js:249:274) at JSmol.min.js:227:389-- I'm using the version: 'Jmol-16.2.1-binary' on Windows 10 OS, 64-bits with latest updates. Chrome version: Version 122.0.6261.129 (Official Build) (64-bit). The error persist in Edge also. I've tried previous version of Jmol (version: Jmol-16.1.63-binary) and the error persist. Can you help me to solve this issue? Best regards,_____________________________________________ Andrei Ionut APOPEI, PhD Associate Professor Curator of the "Grigore Cobălcescu" Museum of Mineralogy and Petrography @ UAIC http://geology.uaic.ro/muzee/mineralogie/ | 3D Minerals & Rocks https://sketchfab.com/MineralogyPetrographyMuseum/collections/rocks-and-minerals http://geology.uaic.ro/andrei.apopei Department of Geology, "Alexandru Ioan Cuza" University of Iasi Carol I st. 11, 700506, Iasi, ROMANIA ¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯ |
From: <m0...@ya...> - 2024-03-16 17:08:02
|
Dear Bob, The following load command load model ({0}) "http://bioinformatics.org/molvis/tmp/consurf/dimer_with_symmetry_header.pdb" filter "!_H;*.CA;*.P;%A;ALLHET;biomolecule 1;bmchains;/=3" fails in 16.1.53 and later releases including 16.2.1.However it works in 16.1.47 and earlier releases.(I did not test releases 48-52). This filter is standard in FirstGlance for large assemblies such as virus capsids. It works with published PDB files having a complete header section. For example this works in 16.2.1: load MODELS ({0}) https://files.rcsb.org/download/7R1C.pdb filter "!_H;*.CA;*.P;%A;ALLHET;biomolecule 3;bmchains;/=3"; spacefill; I suspect that the bug derives from dimer_with_symmetry_header.pdb lacking a complete header section. It has a minimal header, just sufficient for FirstGlance to process its REMARK 350 symmetry operations to generate the biomolecule (see https://bioinformatics.org/firstglance/fgij4.2/notes.htm#dotpdb ). Incidentally, when the command fails in JSmol (in FirstGlance) in Firefox, even after closing the browser tab in which the failure occurred, clicking links in Firefox fails until Firefox is quit and re-started. Because the current public release of FirstGlance (version 4.1) uses JSmol 14.32.69 lacking the bug in question, you can see the desired result in FirstGlance with this link: https://proteopedia.org/wiki/fgij/fg.htm?mol=http://bioinformatics.org/molvis/tmp/consurf/dimer_with_symmetry_header.pdb&bu=1&aunonh=5086&aubb=648&bu2auquotient=110.0000 (This link is automatically generated when you - Paste into the "molecule's URL" slot of FirstGlance http://bioinformatics.org/molvis/tmp/consurf/dimer_with_symmetry_header.pdb - Click on "Functional Assemblies". - Click on "220 chains".) -Eric |
From: Miroslav I. <mir...@gm...> - 2024-03-16 13:11:53
|
Dear Bob, Q1 answer: I found this problem only for this one file, arising from MOPAC calculations of the gold atom, see https://github.com/miroi/stredoskolska-odborna-cinnost-2024/tree/master/orbitaly/atomove_orbitaly/zlato_atom . I wanted to display "true" calculated d-orbitals. But for Silver atom ( https://github.com/miroi/stredoskolska-odborna-cinnost-2024/tree/master/orbitaly/atomove_orbitaly/striebro_atom) and for Copper atom ( https://github.com/miroi/stredoskolska-odborna-cinnost-2024/tree/master/orbitaly/atomove_orbitaly/med_atom) mgf files are fine for Jmol, displaying all (n-1)d (mo 1..5) as well as ns (mo homo) orbitals, plus np virtuals. MOPAC mgf ns orbitals of gold ( https://github.com/miroi/stredoskolska-odborna-cinnost-2024/blob/master/orbitaly/atomove_orbitaly/zlato_atom/zlato_PM7.mgf#L19-L21 ) and of silver ( https://github.com/miroi/stredoskolska-odborna-cinnost-2024/blob/master/orbitaly/atomove_orbitaly/striebro_atom/striebro_PM7.mgf#L20C2-L21C61 ) are seem fine. Something is wrong at Jmol program side. Miro On Fri, 15 Mar 2024 at 23:33, Robert Hanson via Jmol-users < jmo...@li...> wrote: > The integration is a hint that there is a problem here. I also see that > these integrations are not 1.00000+-0.00001, suggesting something odd is > happening. I will look at it after the next (imminent) release. > > I can confirm that this doesn't have any recent origin; even Jmol 14.1 > reads this with the exact same problem. > > Q: Is it only this file? Have you tried others? > Q: If so, what is it about this file that seems to cause it to fail? Maybe > that it is just one atom? > > Bob > > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > |
From: Robert H. <ha...@st...> - 2024-03-16 02:27:58
|
Dear Jmol users, Jmol-16.2.1-binary.zip (63.3 MB) <https://sourceforge.net/projects/jmol/files/latest/download> Moving to a new version set (16.2.x) signals a major update, primarily relating to crystallographic symmetry. This message contains a list of all the new features since 15.2 (15 months ago, about 160). A lot has been added! We basically have a fully functional crystal building capability. This is thanks in no small way to the financial support and enthusiasm provided by the developers of Q-Studio <https://qs.pwmat.com>, a web app specifically geared toward crystal structure building for computational crystallography. The team there has done a fantastic job of building a context around JSmol that makes designing and building crystal structures a snap. Thank you, team! In addition, I want to thank the team at the Bilbao Crystallographic Server <https://www.cryst.ehu.es> for hosting me in Bilbao and patiently guiding me through the process of understanding the nuances of space groups and the mathematics of crystallography. This was critical. So great to work with you! I don't doubt that there are a few bugs here. It was a very complex task getting all the crystal structure building and space group loading and switching working. I encourage those with an interest in teaching about crystallographic symmetry to give some of this a try. I'm already finding it quite enticing, and I think you will, too. I don't think there's ever been a platform like this that allows the *creative design *of powerful, interactive visualizations of this sort. (Publication forthcoming!) The sooner we can find the bugs, the sooner we can get them taken care of. I include here a model of space group 20 and one of its subgroups (ITA 4), with both unit cells indicated, aligned, and packed. You can see that there is a two-fold screw axis common to both; the rest of the symmetry of group 20 has been lost in going to space group 4. The "atoms" are all related to one general position site of space group 20, which has a multiplicity of 8 and were added using the simple command, *modelkit add P wyckoff G*. They are colored based on their site (*color property site)* for space group 4, where the eight-coordinate general position orbit of space group 20 has been split into four pairs of equivalent atoms in space group 4. The additional four atoms in uc-4 fill out the packing of that unit cell. The information needed to create this image, from https://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-tranmax?way=up&super=20&sub=4&index=2&client=maxsub&what=&path=&series=&conj=all&type=t is just the two space group numbers and the unit cell transformation, which in this case is [1/2a+1/2b,c,1/2a-1/2b ; 0,0,0]. The short script used to create this image is WAY down at the bottom of this page. You might be surprised how few lines of script were needed to create this model. Of course, this is a PNGJ file. Enjoy! [image: g20-sg4-w-4-draw-sg-packed.png] I know I am WAY behind on interactive documentation. (Volunteers welcome!!!) Everything I do, though, is described in https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/viewer/Jmol.properties Bob Hanson ----------------------------------------------------------------------------------- Jmol.___JmolVersion="16.2.1" // (legacy) also 16.2.2 (swingJS) bug fix: when unit cells are modified, Symmetry should not be assumed to be unchanged. bug fix: unit cell information should only show space group if symmetry if the unit cell is appropriate bug fix: with set picking SYMMETRY, double-clicks should not start measurements bug fix: LOAD SUPERCELL should retain symmetry-relatad cell as "conventional" new feature: "contrast" color -- for LABEL and ECHO, particularly -- chooses WHITE or BLACK, depending upon the Jmol window background color -- saved in the state as [xfedcba] new feature: set picking SYMMETRY now aliased with set picking SYMOP new feature: MODELKIT SPACEGROUP "HALL:xx xx xx" will create a space group from a Hall or extended Hall description -- future enhancement will allow any HALL description -- see "Space-group notation with an explicit origin", S. R. Hall, Acta Cryst. (1981). A37, 517-525 https://doi.org/10.1107/S0567739481001228 http://macxray.chem.upenn.edu/LATT.pdf thank you, Patrick Carroll http://cci.lbl.gov/sginfo/hall_symbols.html http://cci.lbl.gov/cctbx/explore_symmetry.html new feature: MODELKIT SPACEGROUP ... UNITCELL [a b c alpha beta gamma] PACKED -- after ZAP, creates a new space group with the given unit cell -- optionally packing it, if not after ZAP -- if the unit cell is incompatible with the space group, a similar compatible cell is used version: Version 16.2 represents a major advance in capability for Jmol, particularly in the area of space groups and symmetry in relation to 16.1.1, released 2023.01.24. The following is the listing of 90 new features since then, culled from this file and sorted. More detail on these can be found below. new feature: CONFIGURATION -n new feature: CONFIGURATION "A" new feature: "contrast" color new feature: crystal structure set picking dragMolecule with ALT implemented new feature: DRAW "<hover>xxx</hover>...." new feature: DRAW boundbox $[isosurface id] new feature: DRAW boundbox BEST $[isosurface id] new feature: DRAW HOVERLABEL "xxx" new feature: DRAW SPACEGROUP @a n new feature: DRAW SPACEGROUP @n new feature: DRAW SPACEGROUP ALL new feature: DRAW SYMOP [3,4,5] @1 new feature: ECHO/DRAW with ID starting with "_!_" new feature: Jmol application -A --scriptarguments flag new feature: LOAD "$?" load structure from NCI/CADD with prompt new feature: LOAD "*?" load PDB ID from EBI with prompt new feature: LOAD ":?" load structure from pubChem with prompt new feature: LOAD "=?" load PDB ID from RCSB with prompt new feature: LOAD "==?" load chemical component from RCSB with prompt new feature: LOAD .... fill "rhombohedral" new feature: LOAD .... fill "trigonal" new feature: LOAD =aflowlib/155.2 new feature: LOAD...FILTER "lowPrecision" new feature: LOAD...FILTER "PRECISION=n" where n is up to 16 digits new feature: LOAD - allow CIFReader to ignore COD 2107628 unmodulated operations in presence of modulated new feature: LOAD - AMS reader new feature: LOAD - BilbaoReader allows LOAD ... spacegroup ":n" to force origin, where n is 1 or 2 new feature: LOAD - Binary CIF file structure reading. The BinaryCIF file format new feature: LOAD - CIFReader "ignoreGeomBond" (was SwingJS only) new feature: LOAD - CIFReader FILTER option NOWYCKOFF new feature: LOAD - CIFReader reads atom_site_wyckoff_label new feature: LOAD - CrystalMaker CMDF (binary) file reader new feature: LOAD - Jmol will accept CIF files with duplicate atom_site_label entries new feature: MACRO AFLOW adds SHOWSG(n,i,addSymmetry) new feature: MEASURE .... "default" new feature: MEASURE SELECT ALL new feature: MEASURE SELECT... new feature: MEASURE SELECTED new feature: MEASURE SELECTED ... new feature: MINIMIZE GROUP {atoms} new feature: MINIMIZE ONLY {atoms} new feature: MINIMIZE SELECT {atoms} new feature: MODELKIT ADD <elem> WYCKOFF <Aa-z> new feature: MODELKIT MINIMIZE new feature: MODELKIT MOVETO @atoms @points new feature: MODELKIT SET KEY ON/OFF new feature: MODELKIT SPACEGROUP "HALL:xxxxx" will create a space group from a Hall or extended Hall description new feature: MODELKIT SPACEGROUP "x,y,z;x,-y,z;..." new feature: MODELKIT SPACEGROUP ... UNITCELL ... new feature: MODELKIT VIBRATION WYCKOFF; VIBRATION ON new feature: POLYHEDRA OFFSET {x, y, z} WIGNERSEITZ new feature: POLYHEDRA OFFSET 1.0 BRILLOUIN n where n > 1 new feature: POLYHEDRON LIST new feature: popup menu adds "atom picking..." Drag Atom and Drag Molecule new feature: RESTORE UNITCELL name new feature: SAVE UNITCELL name new feature: SELECT CONFIG=0 new feature: SET minimizationReportSteps new feature: SET picking DRAGMOLECULE for crystal structures new feature: SET picking SYMMETRY now aliased with set picking SYMOP new feature: SET symmetryHM TRUE new feature: SMILES/ALLCOMPONENTS flag for generation of SMILES having multiple components new feature: threaded symmetry-aware UFF minimization of crystal structures. new feature: UFF minimization with application of symmetry for new feature: UNITCELL [a,b,c,alpha,beta,gamma] new feature: UNITCELL RHOMBOHEDRAL and UNITCELL TRIGONAL (or HEXAGONAL - same) new feature: ZAP;MODELKIT SPACEGROUP ... UNITCELL [a b c alpha beta gamma] PACKED new feature: x = (array of SMILES strings).find("SMARTS" or "SMILES", pattern) new feature: x = _args() and _args(n) new feature: x = _arguments and _argumentCount added to SET CALLBACK "jmolscript:..." new feature: x = {*}.find("spacegroup", "parent") new feature: x = {atomset}.atoms and {atomset}.label("%[atoms]") new feature: x = 3x3matrix%1 new feature: x = 3x3matrix%2 new feature: x = atomset.search(pat) new feature: x = compare(A, B, map) and compare(A, B, map, "stddev") new feature: x = function special variables _caller, _callers, _name new feature: x = pattern(<smarts string>) new feature: x = search(target, pattern) new feature: x = spacegroup("ITA/155.1") new feature: x = spacegroup("ITA/ALL") new feature: x = symop("count") new feature: x = symop(matrix,option) new feature: x = symop("wyckoff") new feature: x = symop("wyckoff", "c") new feature: x = symop("wyckoff","C") new feature: x = symop("wyckoff","G") new feature: x = symop("wyckoff","S") new feature: x = @@3.symop("wyckoff",option) new feature: x = {atom}.wyckoff, label %[wyckoff], color PROPERTY WYCKOFF new feature: x = string.pop() new feature: x = string.push("xx") This extends the initial set of 85 new crystallographic features introduced in version 15.2: new feature: CALCULATE POINTGROUP {atoms} new feature: CALCULATE SPACEGROUP new feature: CALCULATE SPACEGROUP {atoms} new feature: CENTER UNITCELL new feature: DRAW HKL {1 1 1 x.x} new feature: DRAW HKL {1 1 1} OFFSET x.x new feature: DRAW INTERCEPT UNITCELL xxx LATTICE {na nb nc}... HKL .... new feature: DRAW intersection [unitcell or boundbox description] [line or plane description] new feature: DRAW intersection [unitcell or boundbox description] LINE @1 @2 new feature: DRAW intersection [unitcell or boundbox description] ON [line or plane description] new feature: DRAW POINTGROUP {atoms} CENTER xx new feature: DRAW UNITCELL xxx LATTICE {na nb nc} new feature: GETPROPERTY unitCellInfo new feature: ISOSURFACE SLAB designations "a=" "b=" "c=" "-a=" "-b=" "-c=" "ab" "bc" "ac" "-ab" "-bc" "-ac" new feature: LOAD .... SPACEGROUP "Hall:P 2y" new feature: LOAD [some crystal structure] filter "POLYMERX" new feature: LOAD [some crystal structure] filter "SLABXY" new feature: LOAD spacegroup 213 unitcell [5 5 5 90 90 90] new feature: LOAD xxxx.mol FILTER "no3D" new feature: LOAD xxxx.mol FILTER "noHydrogen" (Or just "NOH") new feature: MINIMIZE now works (minimally) with a crystal structure. new feature: MODELKIT ON/OFF new feature: MODELKIT ADD "C" point [PACKED] new feature: MODELKIT ADD "Cl" {1/2 1/3 1/3} new feature: MODELKIT ADD "Cl" {1/2 1/3 1/3} PACKED new feature: MODELKIT ADD @1 new feature: MODELKIT ADD @1 "Cl" {1/2 1/3 1/3} new feature: MODELKIT ADD @1 "Cl" {1/2 1/3 1/3} PACKED new feature: MODELKIT ADD @1 "N" new feature: MODELKIT ADD @1 "N" PACKED new feature: MODELKIT ADD @1 PACKED new feature: MODELKIT ADD @2 "C" [PACKED] new feature: MODELKIT ADD @2 [PACKED] new feature: MODELKIT ADD {xxx} PACKED new feature: MODELKIT ADD C [array of points] new feature: MODELKIT ADD/DELETE/MOVETO new feature: MODELKIT CONNECT @1 @2 [0,1,2,3,4,5,p,m] (default 1) new feature: MODELKIT DELETE {atoms} new feature: MODELKIT FIXED NONE new feature: MODELKIT FIXED PLANE plane new feature: MODELKIT FIXED VECTOR point1 point2 new feature: MODELKIT MOVETO @1 {1/2 0 0} new feature: MODELKIT MUTATE new feature: MODELKIT PACKED new feature: MODELKIT ROTATE axis1 axis2 {atoms} degrees new feature: MODELKIT SET autobond true new feature: MODELKIT SET hidden true new feature: MODELKIT SPACEGROUP new feature: MODELKIT SPACEGROUP "P1" new feature: MODELKIT SPACEGROUP 123 new feature: MODELKIT SPACEGROUP 123 packed new feature: MODELKIT SPACEGROUP ... UNITCELL [a b c alpha beta gamma] PACKED new feature: MODELKIT SPACEGROUP "ITA/itno.setting" (e.g. "ITA/155.2") new feature: MODELKIT SPACEGROUP "HALL:xx xx xx" new feature: MODELKIT UNDO/REDO new feature: MODELKIT UNITCELL [unitcell description] new feature: ModelKitCallback new feature: MOVETO AXES [-][ab, bc, ca, ba, cb, ac][1, 2, 3, 4] new feature: plane designations "ab" "ab1" "ac "ac1" "bc" bc1" short for {0 0 1/1 0} {0 0 1/1 c} etc. new feature: set picking dragAtom TRUE now recognizes symmetry for crystal structures new feature: UNITCELL FILL {na nb nc} new feature: UNITCELL OFFSET @1; UNITCELL OFFSET {atoms} new feature: UNITCELL SUPERCELL {na nb nc} new feature: UNITCELL SURFACE {h k l} [height | scale%] [offset or offset%] [TOP] new feature: x = @@1.symop(2, "invariant") new feature: x = @1.pointgroup("spacegroup") new feature: x = @1.symop("invariant") new feature: x = [{point},{point},...].find("equivalent", flags) { new feature: x = {*}.find("spacegroup") -- discovers the space group for a model new feature: x = {*}.find("spacegroup","x,y,-z") new feature: x = {*}.inchi("fixedh?") new feature: x = {*}.inchi("standard") new feature: x = {1/2 1/2 1/2}.symop("invariant") new feature: x = {1/2 1/2 1/2}.symop(2, "invariant") new feature: x = {atoms}.pointGroup() new feature: x = hkl(1 0 0 0.3) to produce plane offset by 0.3 Angstroms from the origin. new feature: x = load(filename, asbinary, async) or load(filename, nbytesMax, async) or load(filename, "JSON", async) new feature: x = search(atomset) new feature: x = spacegroup("123") or spacegroup(123) new feature: x = spacegroup("x,y,z&-x,y,z") or spacegroup("&x,y,z;-x,y,z") or spacegroup("x,y,z;-x,y,z&") new feature: x = spacegroup("x,y,z;-x,y,z") new feature: x = spacegroup("x,y,z;-x,y,z", [a, b, c, alpha, beta, gamma]) new feature: x = spacegroup(6, [a, b, c, alpha, beta, gamma]) new feature: x = symop(2, "invariant") new feature: x = symop(3,@1,"array") adds "xyzNormalized" new feature: ZOOM UNITCELL 0 new feature: ZOOMTO UNITCELL 0 bug fix: changing unit cell using just UNITCELL rather than MODELKIT UNITCELL improperly retains symmetry -- when the unit cell is offset, symmetry should drop to P1 -- when the unit cell is RESET or otherwise returned to the one associated with the space group, symmetry should be returned bug fix: unit cell information displayed should represent the space group accurately -- file-based symmetry initially should reflect the operators from the file -- after MODELKIT SPACEGROUP, the information should reflect a specific setting in Jmol and ITA, if found. new feature: MODELKIT SPACEGROUP ... UNITCELL ... -- adds the ability to set the space group and unit cell at the same time -- unit cell parameters must be compatible with the space group, or the action is aborted -- unit cell can be expressed in one of three formats: -- as the array [a b c alpha beta gamma] -- as the array of cartesian vectors [origin, va, vb, vc} -- as the setting transformation string "a,b,c;0,0,0" new feature: set symmetryHM TRUE -- for show/calculate/draw POINTGROUP -- TRUE switches to Hermann-Mauguin (2m, 2/m2/m2/m) notation -- FALSE switches back to the default Schoenflies (C2v, D2h) notation example script: -- creating a group-subgroup comparison, where the transform between settings is known -- based on information at https://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-tranmax?way=up&super=20&sub=4&index=2&client=maxsub&what=&path=&series=&conj=all&type=t zap modelkit spacegroup 20 draw u20 unitcell color orange mesh nofill "uc-20" modelkit add P Wyckoff G // switching to sg 4 -- note that the listed transform matrix // is for subgroup to supergroup; we need the opposite here, thus the "!" prefix modelkit spacegroup 4 unitcell "!1/2a+1/2b,c,1/2a-1/2b" // drawing unit cell and operations draw uc4 unitcell diameter 0.01 color orange mesh nofill "uc-4" color property site draw id "s12" symop @1 @2 draw id "s43" symop @4 @3 draw id "s56" symop @5 @6 draw id "s87" symop @8 @7 draw id "sg4" spacegroup all //write c:\\temp\\iucr\\g20-sg4-w-4-draw.png as PNGJ // switching back to sg 20: modelkit spacegroup 20 unitcell "1/2a+1/2b,c,1/2a-1/2b" print symop("wyckoff") print {*}.wyckoff.pivot; // switching to sg 4: modelkit spacegroup 4 unitcell "!1/2a+1/2b,c,1/2a-1/2b" print symop("wyckoff") print {*}.wyckoff.pivot; -- 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 *We stand on the homelands of the Wahpekute Band of the Dakota Nation. We honor with gratitude the people who have stewarded the land throughout the generations and their ongoing contributions to this region. We acknowledge the ongoing injustices that we have committed against the Dakota Nation, and we wish to interrupt this legacy, beginning with acts of healing and honest storytelling about this place.* |
From: Robert H. <ha...@st...> - 2024-03-15 22:32:42
|
The integration is a hint that there is a problem here. I also see that these integrations are not 1.00000+-0.00001, suggesting something odd is happening. I will look at it after the next (imminent) release. I can confirm that this doesn't have any recent origin; even Jmol 14.1 reads this with the exact same problem. Q: Is it only this file? Have you tried others? Q: If so, what is it about this file that seems to cause it to fail? Maybe that it is just one atom? Bob |
From: Mark P. <pe...@so...> - 2024-03-15 20:15:54
|
Hi Miroslav, I didn't realize Jmol gave integrations for orbitals. For these unoccupied orbitals it's zero. I wonder if that is causing a problem. auxiliaryInfo.models[1].moData.mos[6].index 6 auxiliaryInfo.models[1].moData.mos[6].occupancy 1.0 auxiliaryInfo.models[1].moData.mos[6].energy -5.7504 auxiliaryInfo.models[1].moData.mos[6].integration 0.000014822299536607877 auxiliaryInfo.models[1].moData.mos[6].coefficients *float[9] [1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0] auxiliaryInfo.models[1].moData.mos[6].spin "alpha" Thanks, Mark On Fri, Mar 15, 2024 at 10:53 AM Miroslav Iliaš <mir...@gm...> wrote: > Hello, > > with MOPAC I calculated the gold atom and printed out the mgf file for > displaying molecular orbitals with the most recent Jmol. > > See > https://github.com/miroi/stredoskolska-odborna-cinnost-2024/tree/master/orbitaly/atomove_orbitaly/zlato_atom > . > > While Jmol console prints mo's 1-5 (occupied 5d-orbitals), for "mo 6" > (6s(1) orbital) it prints > "$ mo 6 > mo 6 invalid! (no atoms selected?)". > > Any help, please ? The gold atom mgf-file, > https://github.com/miroi/stredoskolska-odborna-cinnost-2024/blob/master/orbitaly/atomove_orbitaly/zlato_atom/zlato_PM7.mgf > , seems fine. > > Best, > > Miro > > > > > > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > |
From: Miroslav I. <mir...@gm...> - 2024-03-15 17:53:16
|
Hello, with MOPAC I calculated the gold atom and printed out the mgf file for displaying molecular orbitals with the most recent Jmol. See https://github.com/miroi/stredoskolska-odborna-cinnost-2024/tree/master/orbitaly/atomove_orbitaly/zlato_atom . While Jmol console prints mo's 1-5 (occupied 5d-orbitals), for "mo 6" (6s(1) orbital) it prints "$ mo 6 mo 6 invalid! (no atoms selected?)". Any help, please ? The gold atom mgf-file, https://github.com/miroi/stredoskolska-odborna-cinnost-2024/blob/master/orbitaly/atomove_orbitaly/zlato_atom/zlato_PM7.mgf , seems fine. Best, Miro |
From: Robert H. <ha...@st...> - 2024-03-14 00:34:19
|
You can write startup scripts that change the context menu (right click window) See LOAD MENU but there isn't a way to add toolbar items. Bob |
From: Jose G. <jos...@gm...> - 2024-03-13 12:13:58
|
Greetings, I am new to Jmol. One of the main reasons I would like to use Jmol is to visualize molecular optimization steps as a movie (or MD trajectories). I know one can do that using "Animate", which is under the Tools menu. However, I would like it to be part of the quick access toolbar. Is it possible to customize the toolbar? Thank you, Jose Gascon |
From: John K. <jwk...@al...> - 2024-03-12 17:14:54
|
Thank you all for the v informative replies! I now have several options that I will explore in the coming days. As Otio Rothenberger mentioned, Google Sites is NOT an option for working JSmol webpages. John Keller On Tue, Mar 12, 2024 at 7:15 AM m0lviz--- via Jmol-users < jmo...@li...> wrote: > Dear John, > > Another free web hosting service that supports JSmol (and many other > things) is *bioinformatics.org <http://bioinformatics.org>*. Founded in > 1998 by Jeff Bizzaro and others, it has been in continuous operation since > and now has 35,000 members. It is operated by scilico.com . > > I have had FirstGlance in Jmol at bioinformatics.org for over a decade ( > https://bioinformatics.org/firstglance/fgij/ ). It has been extremely > reliable, however, there were occasional unscheduled outages in 2020, a > couple lasting 8-10 hours. Because these sometimes occurred during the > academic semester, in 2021, I redirected http://firstglance.jmol.org (not > httpS since jmol.org has no certificate) to an installation of > FirstGlance within Proteopedia.Org at https://proteopedia.org/wiki/fgij/ which > is hosted on Amazon Web Services (aws.com; DEEP THANKS to Jaime Prilusky > and Joel Sussman!). As far as I know, this has not had unscheduled > downtime. (However, jmol.org, and therefore the redirect from > firstglance.jmol.org does suffer from occasional downtime.) > > bioinformatics.com remains invaluable to me as an alternate server for > FirstGlance that offers previous versions, a test site for new versions of > FirstGlance, a place to download the open-source code of FirstGlance, a > host for http://atlas.molviz.org , the Jmol Tutorial-Authoring Template > (JTAT, https://www.bioinformatics.org/jmol-tutorials/wiki/ ), an electron > density map tutorial https://www.bioinformatics.org/molvis/edm/ , the > multiple-sequence alignment visualization/analysis tool I developed > https://www.bioinformatics.org/msareveal , and the Proteopedia email list > https://www.bioinformatics.org/mm/listinfo/proteopedialist-for-users . > > -Eric > > > On Monday, March 11, 2024 at 06:32:50 PM EDT, John Keller < > jwk...@al...> wrote: > > > ( Have I asked this before? ) I'm still trying to "embed" or otherwise > insert a jsmol html page in Google Sites. However, when I copy and paste > the html code, Google Sites says "some of the files could not be embedded." > Does anyone know if this has been done successfully somewhere? My > University seems to have stopped providing free space on Apache webservers, > which I suppose is due to the availability of Google Sites. > The campus tech people have not given a definitive answer to this query. > John Keller > > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > |
From: <m0...@ya...> - 2024-03-12 15:15:13
|
Dear John, Another free web hosting service that supports JSmol (and many other things) is bioinformatics.org. Founded in 1998 by Jeff Bizzaro and others, it has been in continuous operation since and now has 35,000 members. It is operated by scilico.com . I have had FirstGlance in Jmol at bioinformatics.org for over a decade ( https://bioinformatics.org/firstglance/fgij/ ). It has been extremely reliable, however, there were occasional unscheduled outages in 2020, a couple lasting 8-10 hours. Because these sometimes occurred during the academic semester, in 2021, I redirected http://firstglance.jmol.org (not httpS since jmol.org has no certificate) to an installation of FirstGlance within Proteopedia.Org at https://proteopedia.org/wiki/fgij/ which is hosted on Amazon Web Services (aws.com; DEEP THANKS to Jaime Prilusky and Joel Sussman!). As far as I know, this has not had unscheduled downtime. (However, jmol.org, and therefore the redirect from firstglance.jmol.org does suffer from occasional downtime.) bioinformatics.com remains invaluable to me as an alternate server for FirstGlance that offers previous versions, a test site for new versions of FirstGlance, a place to download the open-source code of FirstGlance, a host for http://atlas.molviz.org , the Jmol Tutorial-Authoring Template (JTAT, https://www.bioinformatics.org/jmol-tutorials/wiki/ ), an electron density map tutorial https://www.bioinformatics.org/molvis/edm/ , the multiple-sequence alignment visualization/analysis tool I developed https://www.bioinformatics.org/msareveal , and the Proteopedia email list https://www.bioinformatics.org/mm/listinfo/proteopedialist-for-users . -Eric On Monday, March 11, 2024 at 06:32:50 PM EDT, John Keller <jwk...@al...> wrote: ( Have I asked this before? ) I'm still trying to "embed" or otherwise insert a jsmol html page in Google Sites. However, when I copy and paste the html code, Google Sites says "some of the files could not be embedded." Does anyone know if this has been done successfully somewhere? My University seems to have stopped providing free space on Apache webservers, which I suppose is due to the availability of Google Sites. The campus tech people have not given a definitive answer to this query. John Keller |
From: Otie R. <oti...@gm...> - 2024-03-11 23:46:57
|
I'll share our similar experience with you. My colleague Jim Webb and I ran the large lecture section non-major chemistry course at Illinois State University (ISU) - 711 students per semester. We became very dependent on an internal ISU network that was provided by ISU. In early 2000, ISU took this away! I quickly purchased the domains chemagic (com and org) - sorry about that HP! Anyway, we continued this internet work post retirement. Eventually, JSmol was incorporated into this site - the Virtual Molecular Model Kit At one point after retirement, I thought about saving money, so I tried Google Sites. It was a disaster. Completely useless re what we were doing. I stayed with Godaddy, and we (Jim and I) have not looked back. Yes, it's an expense. But Jim and I decided we were going to do this for the rest of our lives. I'm now 81, and it's an important part of my life. Jim and I work on chemagic, which evolved from our ACS Speakers Service years and my Jmol years, every day. I simply made the Godaddy expenses part of my budget, and my pension gives me that and a financially unstressed life - almost 20 years with no financial problems. BTW, I even purchased the domains amibirds.org and amibirds.com for my other hobby - birds of Anna Maria Island. -- Otis Rothenberger oti...@gm... https://chemagic.org > On Mar 11, 2024, at 5:32 PM, John Keller <jwk...@al...> wrote: > > > ( Have I asked this before? ) I'm still trying to "embed" or otherwise insert a jsmol html page in Google Sites. However, when I copy and paste the html code, Google Sites says "some of the files could not be embedded." > Does anyone know if this has been done successfully somewhere? My University seems to have stopped providing free space on Apache webservers, which I suppose is due to the availability of Google Sites. > The campus tech people have not given a definitive answer to this query. > John Keller > > > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users |
From: Luciano A. <luc...@ya...> - 2024-03-11 22:43:50
|
Hello, not answering your questions but possibly a useful suggestion: use altervista.org ... free hosting with PHP, JS, etc. JSmol works perfect.BestLuciano El lunes, 11 de marzo de 2024, 23:32:50 GMT+1, John Keller <jwk...@al...> escribió: ( Have I asked this before? ) I'm still trying to "embed" or otherwise insert a jsmol html page in Google Sites. However, when I copy and paste the html code, Google Sites says "some of the files could not be embedded." Does anyone know if this has been done successfully somewhere? My University seems to have stopped providing free space on Apache webservers, which I suppose is due to the availability of Google Sites. The campus tech people have not given a definitive answer to this query. John Keller _______________________________________________ Jmol-users mailing list Jmo...@li... https://lists.sourceforge.net/lists/listinfo/jmol-users |
From: John K. <jwk...@al...> - 2024-03-11 22:32:18
|
( Have I asked this before? ) I'm still trying to "embed" or otherwise insert a jsmol html page in Google Sites. However, when I copy and paste the html code, Google Sites says "some of the files could not be embedded." Does anyone know if this has been done successfully somewhere? My University seems to have stopped providing free space on Apache webservers, which I suppose is due to the availability of Google Sites. The campus tech people have not given a definitive answer to this query. John Keller |
From: Romuald P. <rom...@un...> - 2024-03-09 19:31:41
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<!DOCTYPE html> <html> <head> <meta http-equiv="content-type" content="text/html; charset=UTF-8"> </head> <body> Dear all<br> did something recently changed in the jsmol-jspecview coupling?<br> It's not working anymore on my website, but turns out to be the same when I'm loading the jsv_jmol.htm example in the jsmol 1.16.63 folder. <br> It returns <br> TypeError: Cannot read properties of undefined(reading 'indexOf') loading file j2s/J/translation/PO.js.J.translation.PO<br> 0 function(c,d,g,h,k)....<br> and then<br> TypeError: Cannot read properties of undefined(reading 'indexOf') loading file j2s/core/coreswing.z.js.JS.AbstractTableModel<br> 0 function(c,d,g,h,k)....<br> <br> I did some additional tests with former versions:<br> same error message with jsmol 16.1.57 or jsmol 16.1.51, but not with jsmol 16.1.47<br> <br> Thank you for your help<br> All the best<br> Romuald<br> </body> </html> |