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 [Jmol-users] Follow up ? From: fziegler - 2017-04-28 23:57:50 Bob: It is my understanding that you have implemented the CIP sub-rule “Z precedes E”. For (4R, 2Z, 5E)-4-methylhepta-2,5-diene, R, E and Z are displayed using the console. But we cannot display R on http://ursula.chem.yale.edu/~chem220/chem220js/STUDYAIDS/isomers/RSEZcombo/RSEZcombo.html E and Z do appear. We use j2s and JSmol.min.js on the website. Is there another file required? Confused in New Haven. Fred 
 Re: [Jmol-users] Jmol 14.15.1 From: Robert Hanson - 2017-04-28 22:39:38 Attachments: Message as HTML Fred, what's your story? I'm reading and writing Gaussian cube files. Example? On Fri, Apr 28, 2017 at 3:29 PM, fziegler wrote: > Bob and Bruce: > > Bruce: Happy to see writing jvxl files working for you. No luck here with > 14.15.1 using Gaussian cube files. Any thoughts. Fred > > > > On Apr 28, 2017, at 2:46 PM, Bruce Tattershall < > bruce.tattershall@...> wrote: > > Bob > > The version you published yesterday works fine for finding chirality in my > organo PS cage compounds > (e.g. with 67 atoms), both in JSmol and in Jmol_S. > > The problem with writing mo jvxl files is also fixed for me. > > Contour plots on a plane .pmesh files do come back with the same colour > scheme they had before saving, > but if one changes this to colour scheme bw, I have not found any way to > switch back to the saved colours, > other than reloading the file. The original isosurface plane was coloured > with colour scheme bwr, but if > I reapply this, the contours come out all white. Any ideas? > > Thanks > Bruce > > *From:* Robert Hanson [mailto:hansonr@... ] > *Sent:* 28 April 2017 19:11 > *To:* jmol-users@... > *Subject:* Re: [Jmol-users] Jmol 14.15.1 > > > OK, that version is broken for CIP chirality determination in JavaScript. > Ran into an odd Java->JavaScript problem that requires recompilation. > Simple structures will work, but more advanced issues will cause atoms to > not display a chirality designation with label %[chirality]. JavaScript > only; Java is fine. > > > Bob > > On Thu, Apr 27, 2017 at 8:41 PM, Robert Hanson wrote: > Jmol.___JmolVersion="14.15.1" // 4/28/17 > > bug fix: values not saved in state for cartoonBlockHeight, cartoonBlocks, > and cartoonSteps > bug fix: write MO broken > bug fix: set cartoonBlockHeight (for DSSR nucleic acid rendering) fails > > new feature: x.split(true) > -- does a white-space token split of the string value of x > > new feature: MOL/SDF reader reads M ISO lines for isotopes > new feature: CIP chirality adds P, S, As, Se, Sb, Te, Bi, Po trigonal > pyramidal and tetrahedral > new feature: CIP chirality adds imine and diazine E/Z chirality > > bug fix: CIP chirality broken for carbonyl groups > bug fix: CIP chirality E/Z should not be indicated for rings of size < 8 > > code: CIPChirality.java 779 lines Rules 1-5 validated on 145 compounds > - see https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/ > Jmol-datafiles/cip/ > code: CIP optimizations > > > > -- > > Robert M. Hanson > Larson-Anderson Professor 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 > 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 > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org ;! > http://sdm.link/slashdot_______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Larson-Anderson Professor 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 
 Re: [Jmol-users] Jmol 14.15.1 From: fziegler - 2017-04-28 20:29:59 Attachments: Message as HTML Bob and Bruce: Bruce: Happy to see writing jvxl files working for you. No luck here with 14.15.1 using Gaussian cube files. Any thoughts. Fred > On Apr 28, 2017, at 2:46 PM, Bruce Tattershall wrote: > > Bob > > The version you published yesterday works fine for finding chirality in my organo PS cage compounds > (e.g. with 67 atoms), both in JSmol and in Jmol_S. > > The problem with writing mo jvxl files is also fixed for me. > > Contour plots on a plane .pmesh files do come back with the same colour scheme they had before saving, > but if one changes this to colour scheme bw, I have not found any way to switch back to the saved colours, > other than reloading the file. The original isosurface plane was coloured with colour scheme bwr, but if > I reapply this, the contours come out all white. Any ideas? > > Thanks > Bruce > > From: Robert Hanson [mailto:hansonr@...] > Sent: 28 April 2017 19:11 > To: jmol-users@... > Subject: Re: [Jmol-users] Jmol 14.15.1 > > OK, that version is broken for CIP chirality determination in JavaScript. Ran into an odd Java->JavaScript problem that requires recompilation. Simple structures will work, but more advanced issues will cause atoms to not display a chirality designation with label %[chirality]. JavaScript only; Java is fine. > > > > Bob > > On Thu, Apr 27, 2017 at 8:41 PM, Robert Hanson > wrote: > Jmol.___JmolVersion="14.15.1" // 4/28/17 > > bug fix: values not saved in state for cartoonBlockHeight, cartoonBlocks, and cartoonSteps > bug fix: write MO broken > bug fix: set cartoonBlockHeight (for DSSR nucleic acid rendering) fails > > new feature: x.split(true) > -- does a white-space token split of the string value of x > > new feature: MOL/SDF reader reads M ISO lines for isotopes > new feature: CIP chirality adds P, S, As, Se, Sb, Te, Bi, Po trigonal pyramidal and tetrahedral > new feature: CIP chirality adds imine and diazine E/Z chirality > > bug fix: CIP chirality broken for carbonyl groups > bug fix: CIP chirality E/Z should not be indicated for rings of size < 8 > > code: CIPChirality.java 779 lines Rules 1-5 validated on 145 compounds > - see https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/cip/ ; > code: CIP optimizations > > > > -- > Robert M. Hanson > Larson-Anderson Professor 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 > 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 > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users 
 Re: [Jmol-users] scripting syntax From: Angel Herráez - 2017-04-28 19:59:24 [I'm moving this to the jmol-users list] Hi Jeff I foresee no problem in your scripts. My advice is that you right-click and open the Console, then paste there your scripted commands one at a time and see which one gives the error or fails to work. On 28 Apr 2017 at 15:15, Jeff Sims wrote: > I´m trying to diagnose scripts written a few years ago that are no longer working in the latest version of JSmol. > The same scripts work correctly in an older version of JSmol: ver. 14.2.4 (2014-08-03). > After updating JSmol, there is no error in the JSmol console, just a blank JSmol canvas (no atoms appear). > > I suspect that it´s syntax related to select´? because nothing is being selected for color or style, but not sure. > > Here are a few excerpts: (I´ll just include an example of each type of call). Does any of this look problematic or need fixes? > I can post the full scripts if helpful. > > model 1 > rotate z -108 > rotate y 130 > rotate z 32 > zoom 100 > restrict not :a and not solvent > > select 147-157 and :a > define switch1a selected > > select switch1a or switch2a or switch3a > define allswitcha selected > > select :i and (177,179,181,192,198,199,200,202,205,211) #numbers are less by 1 than those in the Nature 379 article > define ihb selected #alpha subunit residues hbonding with beta > > elect (switch1b and backbone) and not (173-176) #these sw1b residues interact w/beta > select selected or (177,179,181) and :i > define subset1b selected > > select :a and (172,173,174,176,179,185) or (switch2a and backbone) > define subset2a selected > > select :a > color [xFFAD00] #orange > > select gtp > color [x00C000] #guanine green > > select gdp > color [xFF0000] > > select :i or :b or :g or :d > spacefill on > select atomno=644 and :i > label "\u03b1" > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Jmol-developers mailing list > Jmol-developers@... > https://lists.sourceforge.net/lists/listinfo/jmol-developers --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus 
 Re: [Jmol-users] Jmol 14.15.1 From: Bruce Tattershall - 2017-04-28 18:47:10 Attachments: Message as HTML Bob The version you published yesterday works fine for finding chirality in my organo PS cage compounds (e.g. with 67 atoms), both in JSmol and in Jmol_S. The problem with writing mo jvxl files is also fixed for me. Contour plots on a plane .pmesh files do come back with the same colour scheme they had before saving, but if one changes this to colour scheme bw, I have not found any way to switch back to the saved colours, other than reloading the file. The original isosurface plane was coloured with colour scheme bwr, but if I reapply this, the contours come out all white. Any ideas? Thanks Bruce From: Robert Hanson [mailto:hansonr@...] Sent: 28 April 2017 19:11 To: jmol-users@... Subject: Re: [Jmol-users] Jmol 14.15.1 OK, that version is broken for CIP chirality determination in JavaScript. Ran into an odd Java->JavaScript problem that requires recompilation. Simple structures will work, but more advanced issues will cause atoms to not display a chirality designation with label %[chirality]. JavaScript only; Java is fine. Bob On Thu, Apr 27, 2017 at 8:41 PM, Robert Hanson > wrote: Jmol.___JmolVersion="14.15.1" // 4/28/17 bug fix: values not saved in state for cartoonBlockHeight, cartoonBlocks, and cartoonSteps bug fix: write MO broken bug fix: set cartoonBlockHeight (for DSSR nucleic acid rendering) fails new feature: x.split(true) -- does a white-space token split of the string value of x new feature: MOL/SDF reader reads M ISO lines for isotopes new feature: CIP chirality adds P, S, As, Se, Sb, Te, Bi, Po trigonal pyramidal and tetrahedral new feature: CIP chirality adds imine and diazine E/Z chirality bug fix: CIP chirality broken for carbonyl groups bug fix: CIP chirality E/Z should not be indicated for rings of size < 8 code: CIPChirality.java 779 lines Rules 1-5 validated on 145 compounds - see https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/cip/ code: CIP optimizations -- Robert M. Hanson Larson-Anderson Professor 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 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 
 Re: [Jmol-users] Jmol 14.15.1 From: Robert Hanson - 2017-04-28 18:10:59 Attachments: Message as HTML OK, that version is broken for CIP chirality determination in JavaScript. Ran into an odd Java->JavaScript problem that requires recompilation. Simple structures will work, but more advanced issues will cause atoms to not display a chirality designation with label %[chirality]. JavaScript only; Java is fine. Bob On Thu, Apr 27, 2017 at 8:41 PM, Robert Hanson wrote: > Jmol.___JmolVersion="14.15.1" // 4/28/17 > > bug fix: values not saved in state for cartoonBlockHeight, cartoonBlocks, > and cartoonSteps > bug fix: write MO broken > bug fix: set cartoonBlockHeight (for DSSR nucleic acid rendering) fails > > new feature: x.split(true) > -- does a white-space token split of the string value of x > > new feature: MOL/SDF reader reads M ISO lines for isotopes > new feature: CIP chirality adds P, S, As, Se, Sb, Te, Bi, Po trigonal > pyramidal and tetrahedral > new feature: CIP chirality adds imine and diazine E/Z chirality > > bug fix: CIP chirality broken for carbonyl groups > bug fix: CIP chirality E/Z should not be indicated for rings of size < 8 > > code: CIPChirality.java 779 lines Rules 1-5 validated on 145 compounds > - see https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/ > Jmol-datafiles/cip/ > code: CIP optimizations > > > > -- > Robert M. Hanson > Larson-Anderson Professor 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 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 
 Re: [Jmol-users] Add atom from command line From: Angel Herráez - 2017-04-28 18:09:32 Hi Donna You could probably use set appendNew false load append data ...... See https://chemapps.stolaf.edu/jmol/docs/#set_appendnew https://chemapps.stolaf.edu/jmol/docs/#loadappend https://chemapps.stolaf.edu/jmol/docs/#loaddata https://chemapps.stolaf.edu/jmol/docs/#data --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus 
 [Jmol-users] Fwd: Important MathJax Information From: Robert Hanson - 2017-04-28 17:33:45 Attachments: Message as HTML FYI ---------- Forwarded message ---------- From: Timothy Wallace Date: Fri, Apr 28, 2017 at 12:20 PM Subject: Fwd: Important MathJax Information On April 30th MathJax are closing their self-hosted CDN (Content Delivery Network) services at *cdn.mathjax.org ;* and *beta.mathjax.org ;*. If your colleagues are linking to either of these CDNs for MathJax functionality in any web pages/applications, they will need to change the link(s) to point to an alternative CDN provider. This should be a minor change and details on carrying this out are provided below. *Changing MathJax CDN: *We recommend changing to the cdnjs CDN. MathJax are working with cdnjs to push out future releases. You need to change the link to the CDN wherever it appears in your web page/application code. For example, if you have been using the latest MathJax version (v2.7.0) change the link text before the question mark as below. Note that the url parameters (everything including and after the “?”) should not be changed: ; to This only applies where the CDN is being used to include MathJax functionality. If the MathJax library is being used locally (i.e. has been downloaded and linked to), then no change is required. For further details, please see: https://www.mathjax.org/cdn-shutting-down/ 
 [Jmol-users] Add atom from command line From: Donna Pergin - 2017-04-28 17:23:38 Attachments: Message as HTML So sorry to bother all of you, but I have searched in vain for this. Is it possible to add an atom from the command line (say, to a selected atom)? If so, where is the reference for that? Thanks, Donna Perygin
 [Jmol-users] Jmol 14.15.1 From: Robert Hanson - 2017-04-28 01:42:17 Attachments: Message as HTML Jmol.___JmolVersion="14.15.1" // 4/28/17 bug fix: values not saved in state for cartoonBlockHeight, cartoonBlocks, and cartoonSteps bug fix: write MO broken bug fix: set cartoonBlockHeight (for DSSR nucleic acid rendering) fails new feature: x.split(true) -- does a white-space token split of the string value of x new feature: MOL/SDF reader reads M ISO lines for isotopes new feature: CIP chirality adds P, S, As, Se, Sb, Te, Bi, Po trigonal pyramidal and tetrahedral new feature: CIP chirality adds imine and diazine E/Z chirality bug fix: CIP chirality broken for carbonyl groups bug fix: CIP chirality E/Z should not be indicated for rings of size < 8 code: CIPChirality.java 779 lines Rules 1-5 validated on 145 compounds - see https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/cip/ code: CIP optimizations -- Robert M. Hanson Larson-Anderson Professor 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 
 Re: [Jmol-users] Secondary structure does not match DSSP From: Nicholas Newell - 2017-04-24 15:10:59 Attachments: Message as HTML Understood. Thanks for your replies and for a great program. Nicholas From: Eric Martz Sent: Sunday, April 23, 2017 11:18 AM To: jmol-users@... Subject: Re: [Jmol-users] Secondary structure does not match DSSP Dear Nicholas, Angel is correct. By default, Jmol shows the secondary structure that the authors specified in the PDB file with HELIX, SHEET and TURN records. You will notice that often, authors do not specify TURN records so there are no blue turns initially. After you calculate structure, and color structure, turns are colored blue, and the ends of strands and helices may be different than before. Also, Jmol distinguishes three kinds of helices, and gives them distinct colors: a.. Alpha 3.6(13) b.. 3.0(10) c.. Pi 4.4(16) Each kind is illustrated here in JSmol: http://proteopedia.org/w/Helices_in_Proteins See also http://proteopedia.org/w/Secondary_structure -Eric On 4/23/17 4:56 AM, Angel Herráez wrote: Hi Nicholas However, if I issue the command $calculate structure and then redisplay, the structure is then shown with a ribbon consistent with DSSP, running from 365 to 373. Can anyone tell me why Jmol doesn't display this stretch according to DSSP in the first place? I am not certain, but it is likely that when you load a file Jmol will use the secondary structure declared in the PDB file, and not the DSSP result unless you invoke this later (using calculate). As far as I can interpret, the pdb file says beta strands for Tyr350---Trp356 Cys370---Pro373 so 365-368 are not a beta strand -------------------------------------------------------------------------------- ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot -------------------------------------------------------------------------------- _______________________________________________ Jmol-users mailing list Jmol-users@... https://lists.sourceforge.net/lists/listinfo/jmol-users   Re: [Jmol-users] JSmol labels on zoom From: Jaime Prilusky - 2017-04-24 13:29:45 Thank you Angel! > On 24 Apr 2017, at 13:21, Angel Herráez wrote: > > Hi Jaime > > It's always been like that by default, but I think there is an option: > set fontscaling on > although it is a little tricky to get it working when there is zoom between two > applications of labels. > See https://chemapps.stolaf.edu/jmol/docs/?ver=14.6#font > > > > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users   Re: [Jmol-users] JSmol labels on zoom From: Angel Herráez - 2017-04-24 10:37:10 Hi Jaime It's always been like that by default, but I think there is an option: set fontscaling on although it is a little tricky to get it working when there is zoom between two applications of labels. See https://chemapps.stolaf.edu/jmol/docs/?ver=14.6#font   [Jmol-users] JSmol labels on zoom From: Jaime Prilusky - 2017-04-24 07:29:55 There’s not a proportional change of size of Labels when zooming a model on JSmol 14.9.1 (and maybe on other versions), both on zooming initiated by script and by interactive mouse driven. Labels remain with the original font size despite the change in size of the model. Is there a way to control this? Thank you, Jaim  Re: [Jmol-users] Secondary structure does not match DSSP From: Eric Martz - 2017-04-23 15:18:31 Attachments: Message as HTML Dear Nicholas, Angel is correct. By default, Jmol shows the secondary structure that the authors specified in the PDB file with HELIX, SHEET and TURN records. You will notice that often, authors do not specify TURN records so there are no blue turns initially. After you calculate structure, and color structure, turns are colored blue, and the ends of strands and helices may be different than before. Also, Jmol distinguishes three kinds of helices, and gives them distinct colors: * Alpha 3.6(13) * 3.0(10) * Pi 4.4(16) Each kind is illustrated here in JSmol: http://proteopedia.org/w/Helices_in_Proteins See also http://proteopedia.org/w/Secondary_structure -Eric On 4/23/17 4:56 AM, Angel Herráez wrote: > Hi Nicholas > >> However, if I issue the command$calculate structure and then redisplay, the structure >> is then shown with a ribbon consistent with DSSP, running from 365 to 373. Can anyone >> tell me why Jmol doesn't display this stretch according to DSSP in the first place? > I am not certain, but it is likely that when you load a file Jmol will use the > secondary structure declared in the PDB file, and not the DSSP result unless > you invoke this later (using calculate). > > As far as I can interpret, the pdb file says beta strands for > Tyr350---Trp356 > Cys370---Pro373 > > so 365-368 are not a beta strand > > > 
 Re: [Jmol-users] Secondary structure does not match DSSP From: Angel Herráez - 2017-04-23 08:45:23 Hi Nicholas > However, if I issue the command $calculate structure and then redisplay, the structure > is then shown with a ribbon consistent with DSSP, running from 365 to 373. Can anyone > tell me why Jmol doesn't display this stretch according to DSSP in the first place? I am not certain, but it is likely that when you load a file Jmol will use the secondary structure declared in the PDB file, and not the DSSP result unless you invoke this later (using calculate). As far as I can interpret, the pdb file says beta strands for Tyr350---Trp356 Cys370---Pro373 so 365-368 are not a beta strand --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus   [Jmol-users] Secondary structure does not match DSSP From: Nicholas Newell - 2017-04-22 16:47:29 Attachments: Message as HTML Hello, I'm using Jmol 14.13, which should use the DSSP v2.0 algorithm to compute secondary structure. The command$show defaultStructureDSSP returns true, so this should indeed be the case. However, Jmol displays residues 365-368 from 7odc.pdb as loop-type, not ribbon, while DSSP 2.0 computes this stretch as type E, part of a strand that strectches from residue 365 to residue 373. To complicate matters, at residue 369 Jmol does not not start the ribbon at the residue's nitrogen but instead at its alpha carbon. However, if I issue the command $calculate structure and then redisplay, the structure is then shown with a ribbon consistent with DSSP, running from 365 to 373. Can anyone tell me why Jmol doesn't display this stretch according to DSSP in the first place? It's true that a ramachandran angle calculation does show the stretch 365 to 368 as loop-type with no ribbon, so perhaps for some reason Jmol is doing a ramachandran calculation instead of DSSP for these residues, but then still doesn't explain why the ribbon starts at residue 369's alpha carbon instead of its nitrogen. It's worth noting that this stretch is somewhat ambiguous in secondary structure. Although it shows strand-like H-bonding with an adjacent strand, the chain bends tightly enough at these residues to fit the definition of a beta turn. Does Jmol override DSSP in such cases? Any insight is appreciated. Nicholas Newell  Re: [Jmol-users] Jmol 14.14.1 chirality From: Robert Hanson - 2017-04-22 11:41:40 Attachments: Message as HTML argh. Broke chirality for ketones! On Fri, Apr 21, 2017 at 11:27 AM, Robert Hanson wrote: > > > On Fri, Apr 21, 2017 at 11:10 AM, Bruce Tattershall < > bruce.tattershall@...> wrote: > >> Dear Bob >> >> >> >> The chirality calculation is clearly useful. >> >> >> >> I have tried it on my chiral phosphorus compounds, e.g. as in >> >> https://www.staff.ncl.ac.uk/bruce.tattershall/structs/bpthiq.php >> >> and it finds the chiral carbons in the organic ligands and successfully >> labels them (as R in this case), >> >> but it does not find the chirality of the phosphorus atoms to which they >> are attached. >> >> > It's a work in progress. > > Limitations: > > no parallel chirality paths > not processing inositols correctly > no lone-pair business > standard E/Z, R/S, r/s only; no allenes, no planar asymmetry > > > >> >> I have no idea of how this works, but would it be possible to extend it >> easily to phosphorus chirality (for which >> >> one uses the same rules but counts the lone pair as lowest priority)? >> >> > Lone pairs wouldn't be too difficult to add, particularly if they are > limited to P and S. They are definitely in the IUPAC 2013 spec. I'd like to > add imine stereochemistry as well. > > > >> >> >> When I first got into measuring NMR spectra of diastereomers of such >> compounds about 15 years ago, >> >> I found it very hard to get my inorganic chemist’s head around the >> chirality implications. It would >> >> have been very useful to have a tool to work it out for me. >> >> >> >> If you are going to elements other than carbon, then I guess that besides >> phosphorus, the inorganic >> >> chemist’s favourite, the chirality at silicon, germanium and arsenic >> could also be useful to people. >> > > Silicon and ammonium are just like carbon, I think. As and P no problem. > > Definitely not going to higher valencies any time soon. > > Higher priorities are allenes and getting the darned inositol business > working correctly. But maybe P and S and As are so easy I should just do > them.... > > Bob > -- Robert M. Hanson Larson-Anderson Professor 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   [Jmol-users] R/S-E/Z From: fziegler - 2017-04-21 22:34:01 Attachments: Message as HTML Bob: We have expanded an RS html to include EZ [http://ursula.chem.yale.edu/~chem220/chem220js/STUDYAIDS/isomers/RSEZ/RSEZexercises.html ;]. There are several questions. 1) Can the RS tags be separated from the EZ tags? Just to simplify the display. 2) Is there a reason both sp2 carbons in double bonds are tagged? Is one E/Z tag over the double bond possible? 3) Example (2Z,5E)-4-methyl-2,5-heptadiene displays EZ but not the R-configuration. Exploring this example on the Jmol console, the R-configuration appears. All other examples at the link work fine.   Re: [Jmol-users] Jmol 14.14.1 contour isosurfaces as .pmesh files From: Bruce Tattershall - 2017-04-21 18:24:06 Attachments: Message as HTML Dear Bob I have been trying out your new .pmesh feature. It works well for me, both in JSmol and in Jmol_S. Thanks very much: that solves my timing problems with orbital contour plots in a plane, and I will work on converting the web pages concerned to read in pre-saved isosurfaces instead of calculating them from the orbital data. I will read contours from .pmesh files and orbital surfaces from .jvxl files. The only thing I noticed was that the .pmesh files were rather large at half a megabyte each, for pretty small orbitals with only 21 contours, extending over about 5 Angstroms each. I found that these could be compressed using gzip to about 140 kB, and Jmol_S or JSmol would still read them without obviously more delay. I just wonder whether all that precision is necessary, for models which are only going to be assessed by eye, relatively quickly. I don’t know how easy it is to control numeric output format in the languages you are using, or whether lower precision would be compatible with existing routines for reading .pmesh files. It just occurred to me that if one was going to use this method a lot, it would save server file space and users’ downloads if the files could be a bit smaller. Thanks again Bruce From: Robert Hanson [mailto:hansonr@...] Sent: 20 April 2017 16:47 To: jmol-users@... Subject: Re: [Jmol-users] Jmol 14.14.1 OK - this is better: Looking for the latest version? Download Jmol-14.14.1-binary.zip (69.7 MB) ; On Wed, Apr 19, 2017 at 11:35 PM, Robert Hanson > wrote: hmm. something is missing there. I had to delete that and will upload again. On Wed, Apr 19, 2017 at 11:28 PM, Robert Hanson > wrote: Jmol.___JmolVersion="14.14.1" // released 4/19/17 new feature: WRITE ISOSURFACE "t.pmesh"; WRITE ISOSURFACE "t.pmb" -- creates ASCII (.pmesh) or binary (.pmb) file (a Jmol-specific file format) -- relatively compact format -- can speed up loading of meshes and contours -- for filled surfaces, use .jvxl instead -- read back into Jmol using ISOSURFACE "t.pmesh"/"t.pmb" -- note that binary files are NOT RECOMMENDED for JSmol because some platforms cannot read them locally -- example: load$methane isosurface plane {0 0 0 1} map vdw contours 20 write ISOSURFACE contour.pmb isosurface contour.pmb 
 Re: [Jmol-users] Jmol 14.14.1 chirality From: Robert Hanson - 2017-04-21 16:27:57 Attachments: Message as HTML On Fri, Apr 21, 2017 at 11:10 AM, Bruce Tattershall < bruce.tattershall@...> wrote: > Dear Bob > > > > The chirality calculation is clearly useful. > > > > I have tried it on my chiral phosphorus compounds, e.g. as in > > https://www.staff.ncl.ac.uk/bruce.tattershall/structs/bpthiq.php > > and it finds the chiral carbons in the organic ligands and successfully > labels them (as R in this case), > > but it does not find the chirality of the phosphorus atoms to which they > are attached. > > It's a work in progress. Limitations: no parallel chirality paths not processing inositols correctly no lone-pair business standard E/Z, R/S, r/s only; no allenes, no planar asymmetry > > I have no idea of how this works, but would it be possible to extend it > easily to phosphorus chirality (for which > > one uses the same rules but counts the lone pair as lowest priority)? > > Lone pairs wouldn't be too difficult to add, particularly if they are limited to P and S. They are definitely in the IUPAC 2013 spec. I'd like to add imine stereochemistry as well. > > > When I first got into measuring NMR spectra of diastereomers of such > compounds about 15 years ago, > > I found it very hard to get my inorganic chemist’s head around the > chirality implications. It would > > have been very useful to have a tool to work it out for me. > > > > If you are going to elements other than carbon, then I guess that besides > phosphorus, the inorganic > > chemist’s favourite, the chirality at silicon, germanium and arsenic could > also be useful to people. > Silicon and ammonium are just like carbon, I think. As and P no problem. Definitely not going to higher valencies any time soon. Higher priorities are allenes and getting the darned inositol business working correctly. But maybe P and S and As are so easy I should just do them.... Bob 
 Re: [Jmol-users] Jmol 14.14.1 chirality From: Bruce Tattershall - 2017-04-21 16:10:19 Attachments: Message as HTML Dear Bob The chirality calculation is clearly useful. I have tried it on my chiral phosphorus compounds, e.g. as in https://www.staff.ncl.ac.uk/bruce.tattershall/structs/bpthiq.php and it finds the chiral carbons in the organic ligands and successfully labels them (as R in this case), but it does not find the chirality of the phosphorus atoms to which they are attached. I have no idea of how this works, but would it be possible to extend it easily to phosphorus chirality (for which one uses the same rules but counts the lone pair as lowest priority)? When I first got into measuring NMR spectra of diastereomers of such compounds about 15 years ago, I found it very hard to get my inorganic chemist’s head around the chirality implications. It would have been very useful to have a tool to work it out for me. If you are going to elements other than carbon, then I guess that besides phosphorus, the inorganic chemist’s favourite, the chirality at silicon, germanium and arsenic could also be useful to people. Best wishes Bruce Bruce Tattershall School of Chemistry Newcastle University England From: Robert Hanson [mailto:hansonr@...] Sent: 20 April 2017 16:47 To: jmol-users@... Subject: Re: [Jmol-users] Jmol 14.14.1 OK - this is better: Looking for the latest version? Download Jmol-14.14.1-binary.zip (69.7 MB) ; On Wed, Apr 19, 2017 at 11:35 PM, Robert Hanson > wrote: hmm. something is missing there. I had to delete that and will upload again. On Wed, Apr 19, 2017 at 11:28 PM, Robert Hanson > wrote: Jmol.___JmolVersion="14.14.1" // released 4/19/17 new feature: CALCULATE CHIRALITY {atom set} -- starts with basic CIP Rule 1-2 determination of R/S and E/Z. -- continues with Rules 3-5, which require full-molecule analysis. -- work in progress: -- Rules 1 and 2 complete -- Rule 3 (E/Z) implemented -- Rule 4 partially implemented -- simple linear sequences of R/S ok -- Rule 5 not implemented -- caveates -- no pseudochirality -- not cyclitols -- does not distinguish rings, so inserts "Z" into ring bonds -- only validated on -- optionally limited to the given atom set (or the currently selected atoms by default) 
 Re: [Jmol-users] Jmol 14.14.1 From: Pshemak Maslak - 2017-04-21 15:29:49 Attachments: Message as HTML I can confirm: the command (in bold below) generated the expected closed CAP surfaces in Jmol and JSmol. Thanks Bob, PM On 4/20/2017 10:34 PM, Robert Hanson wrote: > > > On Thu, Apr 20, 2017 at 8:35 AM, Pshemak Maslak > wrote: > > Bob; > > I am looking forward to exploring the new R/S and E/Z > functionality; it's a great addition. > > Does this version include fix for "/*spacefill ionic;lcaocartoon > scale 1.0 CAP unitcell "cpk";spacefill off" */which freezes the > Jmol (Java) and leaves open surfaces (no "cap') on many unticell > faces in JSmol? > > > yes, I think so. Please test. Also the fact that sometimes caps were > not completely closed. > > Thanks, > > PM > > 
 Re: [Jmol-users] Jcamp-mol setup From: PASCAL Andrew - 2017-04-21 13:35:51 Attachments: Message as HTML Looks great, thanks Bob. andy pascal (andrew.pascal@...) ________________________________ From: PASCAL Andrew Sent: 13 April 2017 15:21 To: jmol-users@... Subject: [PROVENANCE INTERNET] Re: [Jmol-users] Jcamp-mol setup That would be great! I'm animating a carotenoid, which is long and thin, so it looks better if it can take the full width of the screen (I want to use it in seminars to illustrate Raman vibrations). On a side note - I seem to have a problem keeping JSpecView properties between sessions. Anything I change is kept if I close and reopen JSV in the same Jmol session, but lost once Jmol is closed and reopened. It also ignores anything I put in Options/Préférences, or into jspecview.properties by hand. andy pascal (andrew.pascal@...) ________________________________ From: Robert Hanson [hansonr@...] Sent: 13 April 2017 15:11 To: jmol-users@... Subject: Re: [Jmol-users] Jcamp-mol setup That said, it's a very good idea, and I'm sure very easy to implement. On Thu, Apr 13, 2017 at 8:11 AM, Robert Hanson > wrote: no, there isn't, but you can adjust the size of that window to anything you want just be dragging the bars around it or resizing the window. On Wed, Apr 12, 2017 at 2:24 PM, PASCAL Andrew > wrote: When connecting a spectrum with a molecular animation in a JCamp-MOL file, is there any way to default to using the main Jmol window for the structure, rather than the JSpecView side panel? Thanks, andy pascal (andrew.pascal@...) ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Jmol-users mailing list Jmol-users@... https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor 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 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 
 Re: [Jmol-users] Jmol 14.14.1 From: Robert Hanson - 2017-04-21 02:34:55 Attachments: Message as HTML On Thu, Apr 20, 2017 at 8:35 AM, Pshemak Maslak wrote: > Bob; > > I am looking forward to exploring the new R/S and E/Z functionality; it's > a great addition. > > Does this version include fix for "*spacefill ionic;lcaocartoon scale 1.0 > CAP unitcell "cpk";spacefill off" *which freezes the Jmol (Java) and > leaves open surfaces (no "cap') on many unticell faces in JSmol? > > yes, I think so. Please test. Also the fact that sometimes caps were not completely closed. > Thanks, > > PM > `

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