Re: [Jmol-users] Message/print echo text?

getproperty shapeinfo is supposed to be delivering that, but it is not. Bug fix On Mon, May 9, 2016 at 11:53 AM, Eric Martz wrote: > Is there a way to message or print (or show) the text currently displayed > at a named echo position? > > For example, something

Re: [Jmol-users] fun with Jmol -- xxxx.find("chemical",...)

On Mon, May 9, 2016 at 11:39 AM, Otis Rothenberger wrote: > Hi Pierluigi- > > For reasons that I do not fully understand, OPSIN returns InChI - not > standard InChI. It does, however, return standard InChIKey! In general, I’d > be very nervous about comparing InChI strings

Re: [Jmol-users] SMILES and SMARTS problems

Ah, yes. Escaping those back-slashes may be the issue. $ load $2-butene C4H8 $ print {*}.find("SMILES","C/C=C/C") ({0:11}) $ print {*}.find("SMILES","C/C=C\C") ({0:11}) $ print {*}.find("SMILES","C/C=C\\C") ({}) So, you see, the real problem is that we are not getting an error message from that

Re: [Jmol-users] Reg: Issue while presenting a 3d model in webpage using jmol export as webpage

ps -- Jonathan? Angel? Any objection to my making that a default? On Mon, May 2, 2016 at 5:31 PM, Robert Hanson <hans...@stolaf.edu> wrote: > Sorry for the delay. ​Your message had to be manually cleared. Probably > what the problem is is that you do not have the JS fi

Re: [Jmol-users] Reg: Issue while presenting a 3d model in webpage using jmol export as webpage

Sorry for the delay. ​Your message had to be manually cleared. Probably what the problem is is that you do not have the JS files required for this project. One thing you can do is to download and extract the jsmol.zip file from the SourceForge Jmol distribution ZIP file. When you do that, you will

Re: [Jmol-users] Flat structures

3D structures obtained from the NCI/CADD Resolver (using *load $xb*) are calculated by a program called CORINA. It doesn't always work, and when it does not, a 2D file is delivered instead. It would be great if NCI would crowd-source the popular 3D coordinate generation in that case, but I

Re: [Jmol-users] Show MEP

If you first use calculate partialcharge then isosurface vdw map mep will work. Jmol will use MMFF94 to do the partial charge calculation. On Sat, Apr 30, 2016 at 12:52 AM, Birgit Lachner wrote: > Dear JSmol/Jmol Friends/Devellopers ... > > I'm very happy to have

Re: [Jmol-users] JSME Fun

he H atoms -- are synchronized. I am almost done with a C13-NMR predictor that works exactly the same way. Bob On Thu, Apr 28, 2016 at 10:34 PM, Robert Hanson <hans...@stolaf.edu> wrote: > Otis, that's very interesting. Nice job on that. I think you are > forgetting, though, that JSME is fully

Re: [Jmol-users] JSME Fun

Otis, that's very interesting. Nice job on that. I think you are forgetting, though, that JSME is fully integrated into JSmol already. You do not need to add any functions of your own. If you look at the code for chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm, you will see that JSME integrates into

Re: [Jmol-users] FW: Directions for converting to JSmol

Excellent! On Sun, Apr 24, 2016 at 8:47 PM, John Keller wrote: > I have many Jmol.js java based. Does this file concatenation approach > gives slower rendering of web pages? Or are there other performance > differences? > no performance issues. Just a translation of the

Re: [Jmol-users] Jmol 14.4.4_2016.04.21

OK - this is fixed. Mainly the issue was that any file with space group symmetry loaded using that symmetry would fail. JmolVersion="14.5.4_2016.04.22" bug fix: on loading, crystallographic file reading fails when applying symmetry bug fix: on loading, user-defined space groups using Hall symbol

Re: [Jmol-users] New iPad

Great news! Thanks, Otis. ​ -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It

Re: [Jmol-users] Background Color

Yes, if you want an RGB triple, use $ print color("RGB",backgroundColor) or for hue/saturation/luminence: $ print color("toHSL",backgroundColor) Bob On Fri, Apr 22, 2016 at 3:55 PM, Otis Rothenberger wrote: > Thanks Rolf, > > I should have known that. It’s

Re: [Jmol-users] Jmol 14.4.4_2016.04.21

hat auth generates the cartoon model and DSSP appears to > do nothing. > > > > On Apr 22, 2016, at 7:40 AM, Robert Hanson <hans...@stolaf.edu> wrote: > > > > sorry, had to delete that build. > > ​ > > > -

Re: [Jmol-users] Jmol 14.4.4_2016.04.21

sorry, had to delete that build. ​ -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications.

[Jmol-users] Jmol 14.4.4_2016.04.21

https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.4/Version%2014.4.4/ Jmol.___JmolVersion="14.5.4_2016.04.21" bug fix: CIF files with missing tags that Jmol needs fail to load at all. (Not necessarily a bad thing, but it is not supposed to fail so dramatically.) bug fix:

Re: [Jmol-users] Application button problems

You want to tell me what the error messages are? But in any case, you are saying that the most recent version works. So what is the question again? On Thu, Apr 21, 2016 at 3:35 PM, Ron Mignery wrote: > Bob, > > On a Windows 10 machine, I download from SourceForge and

Re: [Jmol-users] Application button problems

Hmm. And I was just about to release a new version. I cannot reproduce this issue. Bob On Thu, Apr 21, 2016 at 2:31 PM, Ron Mignery wrote: > Bob, > > In recent releases of the Jmol application, the "center" button no longer > works. Also the "measure" and "select set"

Re: [Jmol-users] window resizer test

; most recently release, all it does is show the platform speed selections. > The applet does not load nor any of the buttons. > > What am I missing? > > Phil > > > > On Apr 20, 2016, at 3:02 PM, Robert Hanson <hans...@stolaf.edu> wrote: > > Oops. No, I just

Re: [Jmol-users] window resizer test

Oops. No, I just didn't realize I had clipped my local path. http://chemapps.stolaf.edu/jmol/jsmol/mmtf.htm One of the things I am trying here is switching to asynchronous transport for binary files. This is *supposed* to be better for compatibility with Safari, but I'm not sure that is the

Re: [Jmol-users] Jmol and MMTF for testing

be sure to clear your cache -- there are a lot of changed files there. On Wed, Apr 20, 2016 at 10:31 AM, Otis Rothenberger <osrot...@icloud.com> wrote: > Your site. > > -- > Otis Rothenberger > o...@chemagic.org > http://chemagic.org > > On Apr 20, 2016, at

[Jmol-users] window resizer test

Please test at file:///C:/jmol-dev/workspace/JSmol/site/jsmol/mmtf.htm the last two buttons on the right. They run the commands: set window 800 800 set window 600 600 -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St. Olaf College Northfield, MN

Re: [Jmol-users] Jmol and MMTF for testing

should be there. I just uploaded another -- http://chemapps.stolaf.edu/jmol/zip/jmol-14.5.4_2016.04.20.zip I'll check into the Mac issue. I think there could be other JSmol issues that are unresolved as well. Bob ​ --

Re: [Jmol-users] Jmol and MMTF for testing

http://chemagic.org > > On Apr 20, 2016, at 9:01 AM, Philip Bays <pb...@saintmarys.edu> wrote: > > Mac Safari does not like the mufti.htm file load from your site. > Unrecognized format for 1crn. Chrome and Firefox work fine. > > > On Apr 20, 2016, at 2:07 AM, Robert

[Jmol-users] Jmol and MMTF for testing

see http://chemapps.stolaf.edu/jmol/jsmol/mmtf.htm and http://chemapps.stolaf.edu/jmol/zip/jmol-14.5.4_2016.04.19.zip needs testing; highly experimental. Bob Jmol.___JmolVersion="14.5.4_2016.04.19" FEATURE NOTE: DSSP calculation at http://www.cmbi.ru.nl/dssp.html as changed

Re: [Jmol-users] RasMol terms

; : 3 "name" : "WC" "nt1" : "|1|D|DG|3" "nt2" : "|1|E|DC|36" } select within(dssr,"pairs") select within(dssr,"pairs[where bp='G-C']") select within(dssr,"pairs[where name=WC']") etc.

Re: [Jmol-users] RasMol terms

about how to get that working again. On Thu, Apr 14, 2016 at 12:59 PM, Rolf Huehne <rolf.hue...@leibniz-fli.de> wrote: > On 04/14/2016 07:19 PM, Robert Hanson wrote: > > Phil, you should check out DSSR. It is amazing! Sorry this is not > > documented yet: > > > > new

Re: [Jmol-users] RasMol terms

Phil, you should check out DSSR. It is amazing! Sorry this is not documented yet: new feature: select shortcuts for nucleic acid structures -- for example: select junctions; select kissingloops -- activated after load =/dssr or calculate structure dssr -- includes: "@bulges

Re: [Jmol-users] Jmol-14.4.4_2016.04.13 released

ps. see https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.4/Version%2014.4.4/ ​ -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance

[Jmol-users] Jmol-14.4.4_2016.04.13 released

Jmol.___JmolVersion="14.5.4_2016.04.13" bug fix: JSmol cannot load RCSB ligand files bug fix: "axis" unintentionally made reserved word in "14.4.4_2016.03.19" bug fix: symop(@1 @2) broken bug fix: symop() taking default unitcell from "current" -- should be that it REQUIRES a prefix

Re: [Jmol-users] Jmol 14.4.4_2106.04.11

cial test with both jsmol.htm and test2.htm. > Heme does not load. Get an unrecognized file type. Works fine in the 0331 > update. Other RCSB links work fine. > > Safari and Firefox on Mac on local network. > > > Phil > > > On Apr 11, 2016, at 7:44 PM, Robert Hans

Re: [Jmol-users] Cannot load PDBs from RCSB in Chrome -used to work

The reason I opted for /view/ instead of /download/ is that its header for /download/ is Content-Type: application/octet-stream whereas with /view/ it is Content-Type: text/plain;charset=UTF-8 This makes sense, as "download" initiates in the browser exactly that -- a download (save to file).

Re: [Jmol-users] Nascam results visualisation

no idea. You would have to send me the actual data file. On Wed, Apr 13, 2016 at 12:27 PM, Ürmös Antal wrote: > Dear All, > > I write to you, after some months effort. I would like to ask, that > which program and which hardware configuration do you use for

[Jmol-users] Jmol 14.4.4_2106.04.11

Jmol.___JmolVersion="14.4.4_2016.04.11" bug fix: qchem reader fails to switch to spherical D/F basis for second structure bug fix: pointGroup secondary axis in yellow is too hard to see -- using "orange" instead new feature: symop() options: symop(op) -- returns the 4x4 matrix

Re: [Jmol-users] Cannot load PDBs from RCSB in Chrome -used to work

Hmm. That was supposed to read: I notice that http://www.rcsb.org/pdb/files/1xpb.pdb is giving a 301 move-permanently redirect. It's possible that Firefox can handle that in AJAX but Chrome cannot. These are getting re-directed to http://files.rcsb.org/download/1xpb.pdb ps - there is no need to

Re: [Jmol-users] Cannot load PDBs from RCSB in Chrome -used to work

I notice that http://www.rcsb.org/pdb/files/1xpb.pdb is giving a 301 move-permanently redirect. It's possible that Firefox can handle that in AJAX but Chrome cannot. These are getting re-directed to http://www.rcsb.org/pdb/files/1xpb.pdb I have added into JSmol the capability of automatically

Re: [Jmol-users] How to show a cross-section of an isosurface?

Please send one of these to hans...@stolaf.edu If it is a format Jmol can read, it would be isosurface "lead.bxsf" then isosurface slab On Wed, Apr 6, 2016 at 6:43 AM, Vincent Sacksteder wrote: > Dear Robert and jmol list, > > thank you for your help about doing

Re: [Jmol-users] How to show a cross-section of an isosurface?

Just slab it from both sides with a thin shell in between. You could also plot the "heat map" of the isosurface onto the plane. But perhaps you don't need that. load C6H6.smol isosurface molecular map mep isosurface slab none slab plane {0 0 1 -0.05} slab plane {0 0 -1 -0.05} [image: Inline

Re: [Jmol-users] Load Spartan Default on Jmol Docs Page

I have changed the documentation to read: SPARTAN *FILTER "MULLIKEN"* loads Mulliken charges rather than the default ESP charges. (ESP charges are better for displaying molecular electrostatic potential maps using *isosourface molecular map MEP*.) ​

Re: [Jmol-users] Protein Loading

Drag-drop can't utilize jsmol.php, because it is not a "file" per se, just a bunch of bytes. But try it in your installation at http://sites.saintmarys.edu/~pbays/ -- worked for me there Bob ​ -- Transform Data into

Re: [Jmol-users] Protein Loading

On Fri, Apr 1, 2016 at 2:52 PM, Philip Bays wrote: > I have a file entitled 5e6e.pdb.gz that I downloaded this week. Using > previous versions of jsmol.min, this file would load via drag-and-drop or > using the local-file load mechanism. In the latest version, jsmol version

[Jmol-users] Jmol 14.4.4_2016.03.31

Jmol.___JmolVersion="14.4.4_2016.03.31" released *bug fix: load $ broken; http://cactus --> https://cactus *bug fix: _geom_bond_distance starting with "." halts CIF file reading Looking for the latest version? * Download Jmol-14.4.4_2016.03.31-binary.zip

Re: [Jmol-users] NCI resolver down -- IMPORTANT

Note: New jsmol.min.js, jsmol.lite.js, jsmol.min.nojq.js, jsmol.lite.nojq.js are all to be found in http://chemapps.stolaf.edu/jmol/jsmol This fixes the problem of the shift from http:// to https:// at NCI. Very sorry for the inconvenience. Bob ​

[Jmol-users] NCI resolver down -- IMPORTANT

As of this moment, at least, load $ fails with the following message. I am looking into it. Basically, though, you need to use https instead of http. Hopefully this is just a switch that can be un-thrown. If not, all sites utilizing this short-cut will need updating. If you need to do a

Re: [Jmol-users] SMILES Problem with 14.4.4_2016.03.25

yyy) { ; } } instead of if () { break; } if (yyyy) { ; } On Tue, Mar 29, 2016 at 9:01 PM, Robert Hanson <hans...@stolaf.edu> wrote: > shoot

Re: [Jmol-users] SMILES Problem with 14.4.4_2016.03.25

shoot! Thanks for testing, Otis... ​ -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more.

Re: [Jmol-users] get java object questions

string and using the split on comma trick. > > Otis > > -- > Otis Rothenberger > o...@chemagic.org > http://chemagic.org > > On Mar 29, 2016, at 8:36 AM, Robert Hanson <hans...@stolaf.edu> wrote: > > I have no idea. What are you trying to do? > > For mol

Re: [Jmol-users] JSmol

Sounds about right. You cannot tell that you are not using Java, except for the performance. The Java language is being implemented *as* JavaScript. x = new java.util.Hashtable() Object { elementCount: 0, elementData: Array[11], loadFactor: 0.75, threshold: 8, firstSlot: 11, lastSlot: -1,

Re: [Jmol-users] Jmol use

The collecting is done only when the applet is fully loaded. So perhaps a crawler could not activate that.​ It would have to load all the JavaScript and see an active model. -- Transform Data into Opportunity. Accelerate

Re: [Jmol-users] Open local files

"Open Local File" is not a Jmol script command. Check http://chemapps.stolaf.edu/jmol/jsmol/simple2.htm to see how the "Load File" link works. I believe it is just load ? On Tue, Mar 29, 2016 at 1:02 PM, Philip Bays wrote: > I am putting together a page and want a link

Re: [Jmol-users] Jmol use

no adjustment. I don't know how to do that. OK, so "real" is an ambiguous term here ​ -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library.

Re: [Jmol-users] Java 77 failing in Firefox on Mac

I am not having this problem in Firefox with Java 1.8.077. Sorry, can't help you! ​ -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to

[Jmol-users] Jmol use

Wow, this is for real. Since Jan, 2014, recorded use of JSmol: [image: Inline image 1] -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it

Re: [Jmol-users] one more try....

Excellent, Otis. Do let me know if Salem finds anything else. Now we know that the CACTVS SMILES algorithm allows C1(C) both C(C)1, but in the case where you have /1 (or \1), that MUST be C/1(C), not C(C)/1. Since Jmol was always generating branches before connections (because it's the branching

[Jmol-users] one more try....

Looking for the latest version? *Download Jmol-14.4.4_2016.03.25-binary.zip (61.2 MB) * Fixes Jmol.evaluateVar() and Jmol.getPropertyAsArray() Right, Otis? Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry

Re: [Jmol-users] Ouch!

Ah, and here's our problem. When I fixed the \1 business, I broke standard strings! Jmol.getPropertyAsJSON(jmolApplet0,"moleculeInfo") "{"moleculeInfo": [ { "nElements": 20,"numberInModel": 1,"mf": *H 10 C 8 N 4 O 2*,"number": 1,"modelNumber": 1.1,"nAtoms": 24 } ]}" That did not get put into

Re: [Jmol-users] Ouch!

It's something about how I am converting these to JSON and then from there evaluating them. Otis, here's something to sink your teeth into. Forget JSON or JavaScript - now you can directly read that info as a "Java" object: x = Jmol.getPropertyAsJavaObject(jmolApplet0,"moleculeInfo")

Re: [Jmol-users] Ouch!

spin) -- n trails are made, typically in a fan-like pattern that trails the spinning vector load =magndata/1.1.37 set vectortrace 20 set vibrationperiod 2 vibration on new feature: unitcell ON adds #nnn (international table number) to cell description if found On Thu, Mar 2

Re: [Jmol-users] Ouch!

Still having problems with this build. I have removed 03.24b as well. On Thu, Mar 24, 2016 at 11:17 AM, Robert Hanson <hans...@stolaf.edu> wrote: > I have removed all versions of Jmol made after March 20, because of the > problem of their improperly saving the state of boundb

Re: [Jmol-users] SMILES problem

Yeah, today is "fix-it" day all day. OK. The aspirin Java error is fixed. The other error has to do with the fact that we are returning "\1" inside a string. I'll have to track down where that is coming from. Can't work on this for a bit Bob On Thu, Mar 24, 2016 at 2:23 PM, Otis

Re: [Jmol-users] Ouch!

See * Download Jmol-14.4.4_2016.03.24b-binary.zip (61.0 MB) *​ Jmol.___JmolVersion="14.4.4_2016.03.24b" released NOTE: This release replaces 03.21, 03.22, and 03.24, which I have deleted on SourceForge because

[Jmol-users] Ouch!

I have removed all versions of Jmol made after March 20, because of the problem of their improperly saving the state of boundbox, unitcell, and axes when those are set using, for instance using UNITCELL 0.1 Recompiling and updating now. Sorry for the inconvenience. Bob

Re: [Jmol-users] fun with Jmol -- xxxx.find("chemical",...)

the structure will be > the same the student has drawn. A bit more complicated, but the students > could improve their ability in writing formulas correctly and naming them. > > I will elt you know about the improving of my site. > > Thanks again and bye! > > Pierluigi > &g

Re: [Jmol-users] Resolver SMILES input errors

got it! I have made changes to Jmol and JSmol to direct PDB default loading to be from files.rcsb.org see https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.4/Version%2014.4.4/ * Download Jmol-14.4.4_2016.03.24-binary.zip (61.2 MB)

Re: [Jmol-users] New path for RCSB files causes Jmol error

I have made changes to Jmol and JSmol to direct PDB default loading to be from files.rcsb.org see https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.4/Version%2014.4.4/ * Download Jmol-14.4.4_2016.03.24-binary.zip (61.2 MB)

Re: [Jmol-users] fun with Jmol -- xxxx.find("chemical",...)

Nothing stops you from adding that to your pages, Pierluigi! :) In answer to the question, the name/SMILES, SMILES/name and SMILES/structure conversion is going through the NCI CACTVS resolver, which is just a fantastic resource. structure/SMILES conversion is done within Jmol unless it is

Re: [Jmol-users] Retrieve Temperature Factor Annotation via JMOL API

Charles, I would be more than happy to help you with that. Give me a hint at hans...@stolaf.edu what you have going right now for the other data, and I will fill you in. Bob ​ -- Transform Data into Opportunity.

Re: [Jmol-users] New path for RCSB files causes Jmol error

The issue is that JSmol.min.js doesn't recognize your new url as one that can be used for direct AJAX transfer. If you want to fix this yourself, look in JSmol.min.js for "www.rcsb.org":"%URL", or "www.rcsb.org":null, and ADD to that a similar entry for files.rcsb.org ​

Re: [Jmol-users] Resolver SMILES input errors

On Wed, Mar 23, 2016 at 10:15 AM, Otis Rothenberger wrote: > Bob, > > C(\C)/1=C/C=C.C\1=C > > Resolver cannot read this, and I’m now thinking that it’s, understandably, > geometry confused. I don’t know how to read these things, so I’m not sure. > Interestingly, if I send

Re: [Jmol-users] trans fatty acids

On Tue, Mar 22, 2016 at 11:05 AM, Otis Rothenberger wrote: > Hi Richard, > > That model is coming from Resolver. Resolver does not use MM to compute 3d > models. Basically, the steps are as follows: > > 1) The connection identifier (SMILES, InChI, IUPAC, etc) is broken down

[Jmol-users] fun with Jmol -- xxxx.find("chemical",...)

Did you know that this is now possible in Jmol: $ print "C1=CC=CC1=O".find("chemical","name") cyclopenta-2,4-dien-1-one $ print "succinic anhydride".find("chemical","SMILES") O=C1CCC(=O)O1 $ print "maleic anhydride".find("chemical","SMILES") O=C1OC(=O)C=C1 $ print "maleic

Re: [Jmol-users] Invert Stereochemistry Seems to be Broken

Happy to report this was a very recent break - about two weeks ago, due to some recent work on SMILES. Fixed now. Looking for the latest version? * Download Jmol-14.4.4_2016.03.22-binary.zip (61.2 MB) *

Re: [Jmol-users] Jmol 14.4.4_2016.03.21

I am not seeing that. Others? ​ -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more.

[Jmol-users] Jmol 14.4.4_2016.03.21

This update takes care of a few minor bugs and also introduces several powerful features in relation to polyhedra, unit cells, and SMILES. Jmol.___JmolVersion="14.4.4_2016.03.21" released new feature: moveto axis [a1-c4] -- extends moveto axis a|b|c to all for corners 1|2|3|4 where 1 is

Re: [Jmol-users] Invert Stereochemistry Seems to be Broken

s all Safari and FF. > > Otis > -- > Otis Rothenberger > o...@chemagic.org > http://chemagic.org > > > On Mar 18, 2016, at 8:46 AM, Robert Hanson <hans...@stolaf.edu> wrote: > > > > I need a script that I can run, please. > > ​ > > &

Re: [Jmol-users] Invert Stereochemistry Seems to be Broken

could be...I was working on that. Can you give me a script that is failing? ​ -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn

Re: [Jmol-users] Invert Stereochemistry Seems to be Broken

I need a script that I can run, please. ​ -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more.

[Jmol-users] Jmol 14.4.4 released

see https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.4/Version%2014.4.4 New features include: -- more SMILES/SMARTS options, including OpenSMILES, Strict Hueckel 4+2, and MMFF94 options. show smiles/open show smiles/strict show smiles/mmff94 show smiles/noaromatic InChI.js library

Re: [Jmol-users] Malware

Nothing to do with Jmol. I'm guessing it is this: https://www.symantec.com/security_response/writeup.jsp?docid=2003-102718-1528-99 ​ -- Transform Data into Opportunity. Accelerate data analysis in your applications with

Re: [Jmol-users] new InChI option

Otis, have you noticed any performance issues with the InChI add-on? I ask because when I was debugging it, I noticed that it was using a 16.5MB integer array. I'm guessing that's the program's working heap space. Pretty impressive. On Thu, Mar 10, 2016 at 11:51 AM, Robert Hanson <h

Re: [Jmol-users] new InChI option

On Thu, Mar 10, 2016 at 10:33 AM, Otis Rothenberger wrote: > Bob, > > I currently get my non-stereo inchi’s by having JME load the Jmol > extracted molfile. Then I use the resulting JME non-stereo SMILES to get > the the non-stereo inchi from Resolver or ChemSpider's inchi

Re: [Jmol-users] new InChI option

On Thu, Mar 10, 2016 at 9:12 AM, Otis Rothenberger wrote: > Bob, > > Very nice, thanks! > > I still have a problem on first load, and I assume this has to do with the > async load of inchi.js. > Just make sure you do not automatically call for an inchi. Make sure it is a

Re: [Jmol-users] new InChI option

error: undefined is not an object (evaluating "a.stack") > > I guess I can understand why that taxol molfile breaks the app. It's a > mess. I'd just like to catch this situation before the 3rd load break > starts. > > Oh yeah, the first page load after a cache clear almos

Re: [Jmol-users] new InChI option

OK, so there are some bugs there. And loading trashy 2D files is definitely a bad idea. Otis, can you figure out the way to report this sort of thing? ​ Bob -- Transform Data into Opportunity. Accelerate data analysis in

Re: [Jmol-users] new InChI option

from > NCI/CADD)"); > > calc = > InChI.fromMolfile(Jmol.evaluateVar(jmolApplet0,"write('MOL')")).trim(); > > $("#inchi1div").html(calc + "(calculated > in JavaScript)"); > > $("#log").html(nci==calc ? "no difference&quo

Re: [Jmol-users] new InChI option

Otis, note that there is a bug there. If you ask for the models in this order: $taxol $morphine inchi.js seems to hang and just never respond. Something to do with the fact that $taxol is pathologically 2D and not 3D. But $taxol $methanol works, until you ask for $morphine. Then it hangs. Go

Re: [Jmol-users] new InChI option

look > into this stdinchi capability. > > Otis > > -- > Otis Rothenberger > o...@chemagic.org > http://chemagic.org > > > On Mar 7, 2016, at 1:44 PM, Robert Hanson <hans...@stolaf.edu> wrote: > > > > Thanks, Otis -- I forgot that there were two InChI calls

Re: [Jmol-users] new InChI option

Thanks, Otis -- I forgot that there were two InChI calls for NCI -- "inchi" and "stdinchi". Changing that makes them identical. ​ Bob -- Transform Data into Opportunity. Accelerate data analysis in your applications with

Re: [Jmol-users] "Unrecognized file format for file ..."

It's very important to do this test. Please report what you find. On Sun, Mar 6, 2016 at 11:25 AM, Robert Hanson <hans...@stolaf.edu> wrote: > If you open a console and instead use > > print load(".file name...") > > then you will see the contents of that file

[Jmol-users] new InChI option

http://chemapps.stolaf.edu/jmol/jsmol/inchi.htm demonstrates a new option - calculating an InChI in JavaScript from a JSmol model. The InChI code is a bit heavy -- 800K. Interesting to compare with what NCI/CADD returns. Necessary files are in http://chemapps.stolaf.edu/jmol/jsmol/inchi The

Re: [Jmol-users] "Unrecognized file format for file ..."

If you open a console and instead use print load(".file name...") then you will see the contents of that file. Or, for that matter, you just do that in your browser. That is a standard result of getting an HTTP "File Not Found" message from the server. On Sat, Mar 5, 2016 at 9:21 PM, Rojan

Re: [Jmol-users] jsmol does not activate molecule automaticaly (moodle)

See https://docs.moodle.org/30/en/Jmol_filter where it indicates that you need to add a search item ?i=0 to your URL: *?i=0* results in the interactive structure being displayed directly (i.e. with no cover image). This may result in page load delays if, say, multiple Jmol objects are present in

[Jmol-users] jmol-14.4.3_2016.03.05.zip

http://chemapps.stolaf.edu/jmol/zip/jmol-14.4.3_2016.03.05.zip Jmol.___JmolVersion="14.4.3_2016.03.05" bug fix: SMILES TB trigonal bipyramidal stereochemistry not functional bug fix: SMILES [@TBn] not recognizing n > 2 bug fix: SMILES OH octahedral stereochemistry error bug fix: SMILES [@OHn]

Re: [Jmol-users] Side effect of set echo all

good catch; simple fix -- see http://chemapps.stolaf.edu/jmol/zip/jmol-14.4.3_2016.03.03.zip ​ -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at

[Jmol-users] JmolVersion="14.4.3_2016.03.02"

https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.4/Version%2014.4.3/ * Download Jmol-14.4.3_2016.03.02-binary.zip (60.9 MB) * Jmol.___JmolVersion="14.4.3_2016.03.02" bug fix: JavaScript reference to j2s for

Re: [Jmol-users] Jmol 14.4.3_2016.02.27

I have placed a revised JSmol.min.js at http://chemapps.stolaf.edu/jmol/zip/JSmol.min.js On Mon, Feb 29, 2016 at 3:55 PM, Robert Hanson <hans...@stolaf.edu> wrote: > OK, so there are four images now: > > Info.coverImage provided by user if desired; no default >

Re: [Jmol-users] Try / catch not working for file loading

atch(e) { print "load() error: " + e } Bob My feeling is that On Mon, Feb 29, 2016 at 5:11 PM, Rolf Huehne <rolf.hue...@leibniz-fli.de> wrote: > Am 29.02.16 um 23:10 schrieb Robert Hanson: > > I believe that is the correct behavior. It's just that in the case of > &g

Re: [Jmol-users] Try / catch not working for file loading

I believe that is the correct behavior. It's just that in the case of the JavaScript version of the applet you get an HTML error message, and in Java you get a Java error message. Your code is just printing that error message (fileData). But I see. you were expecting load("") to throw an

Re: [Jmol-users] Jmol 14.4.3_2016.02.27

OK, so there are four images now: Info.coverImage provided by user if desired; no default appletLoadingImageJSmol_spinner.gif Info.makeLiveImageplay_make_live.jpg (no Info option)cursor_wait.gif There's a bug there where JSmol is pointing to the page's j2s/

Re: [Jmol-users] cyclic peptide trace?

I considered it a bug. Jmol.___JmolVersion="14.5.3_2016.02.28" bug fix: cyclic peptides do not complete loop for cartoons, backbone, etc. (1SFI) * Download Jmol-14.4.3_2016.02.28-binary.zip (60.9 MB) * On Tue, Feb 16,

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