Re: [Jmol-users] Jsmol for mobile

What is the "desktop option"?​ -- Monitor 25 network devices or servers for free with OpManager! OpManager is web-based network management software that monitors network devices and physical & virtual servers, alerts via e

Re: [Jmol-users] stopping scripts

sending the script !quit should stop your script. On Tue, Jun 23, 2015 at 2:00 PM, Pshemak Maslak wrote: > It looks like my previous post got lost: > > To showcase a crystal structure we have a longish "tour" script composed > of several moveto, rotate, adding and removing labels, changing >

Re: [Jmol-users] Unable to save session file

When I try this in Firefox or Chrome it works fine. A file name is requested, and then I get a download notice that the file has been created. What browser are you using? -- Monitor 25 network devices or servers for free w

Re: [Jmol-users] JSME Qestion

ese demos. I can, in fact, write > code that loads just jsme, and the applet works as expected in Safari and > Firefox. Still having some issues with Chrome (i.e. blank screen!). > > > > > On Jun 18, 2015, at 7:58 PM, Robert Hanson wrote: > > > > > > ​I ha

Re: [Jmol-users] script variables treated differently in headless version than in application?

Exactly. That's why you need the -J option in this case. So that "$CC" is being passed to the script as a parameter. If you want to also load that file, use: java -jar "%JMOL_HOME%\JmolData.jar" -ion $CC -J "headless.spt('$CC')" alternatively, you can recover "$CC" as molUnit = getProperty("au

[Jmol-users] jmol-14.3.15_2015.06.19.zip

http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.15_2015.06.19.zip Jmol.___JmolVersion="14.3.15_2015.06.19" bug fix: msCIF reader can hang if occupancy is not fractional bug fix: JSmol applet not returning full set of parameters in animFrameCallback bug fix: load FILL command can fail if base unit c

Re: [Jmol-users] script variables treated differently in headless version than in application?

Jmol is not set up to load arguments into -s headless.spt While that is an interesting option, it's just not there. I think the thing to do is use -J instead of -s. This will run an in-line script, which can then call your headless.spt script with a parameter: java -jar "%JMOL_HOME%\JmolData.jar"

Re: [Jmol-users] JSME Qestion

​I have increased the width of the JSME applet to be 350, even if I do like squares. :) Thanks, Angel. -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://li

Re: [Jmol-users] msCIF problems

'm still seeing render errorjava.lang.NullPointerException for > two out of my collection of 60+ msCIFs > The other one is > > http://scripts.iucr.org/cgi-bin/sendcif?ck5035 > > NB. it renders OK if I load with FILTER "MODAVERAGE" > so I can at least work round this > > Cheers > &g

Re: [Jmol-users] FirstGlance in Jmol 2.3 released

Eric, that's great. Are you utilizing Jmol's very powerful annotation features? These allow you access to the full information in the PDB validation suite, including close contacts, bad angles, and much more. It uses the /val extension and gets its information from EBI. $ load =1crn/val *

Re: [Jmol-users] appletReadyCallback destroys the Jmol object?

Ah -- right -- Info.readyFunction is the one to use. Perhaps we should abandon the readyCallback. I think JSmol uses it itself. By using it yourself, you cancel code that JSmol needs to finalize the loading. (And perhaps start more applets loading) On Tue, Jun 16, 2015 at 12:40 PM, Angel Herráe

Re: [Jmol-users] mo cut off

Yes, that is what it means. On Tue, Jun 16, 2015 at 7:00 AM, Ward Poelmans wrote: > Hi, > > I've got a question about the cut off for plotting molecular orbitals > and isosurfaces. I want to plot my orbitals from a molden file and I > noticed that molden and Jmol need a different cut off value t

Re: [Jmol-users] msCIF problems

superspace model, I still get nothing. > Java console gives: ...render errorjava.lang.NullPointerException > > Cheers > > Simon > > > > > Quoting Robert Hanson : > > > I checked with Vaclav, and he agrees that the file is inval

Re: [Jmol-users] msCIF problems

still get nothing. > Java console gives: ...render errorjava.lang.NullPointerException > > Cheers > > Simon > > > > > Quoting Robert Hanson : > > > I checked with Vaclav, and he agrees that the file is invalid. > > > &

Re: [Jmol-users] Jmol - cool crystallography capabilities

Make that http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.15_2015.06.14c.zip something odd in the compilation of that 14b version. ​ -- ___ Jmol-users mailing list Jmol-users@lists.

Re: [Jmol-users] Jmol - cool crystallography capabilities

ps -- I failed to upload that last night -- it is there now. On Mon, Jun 15, 2015 at 2:42 AM, Robert Hanson wrote: > http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.15_2015.06.14b.zip > > testing appreciated -- I would like to release a new version of Jmol 14.2 > before the end

[Jmol-users] Jmol - cool crystallography capabilities

http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.15_2015.06.14b.zip testing appreciated -- I would like to release a new version of Jmol 14.2 before the end of the week. Jmol.___JmolVersion="14.3.15_2015.06.13" bug fix: var firstPARAM = "p1_b"; x = [FIRSTParam: "p1_a"]; results in lowering of case

Re: [Jmol-users] Function call with hash parameter - case conversion

This is fixed http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.15_2015.06.14b.zip On Mon, Jun 15, 2015 at 12:33 AM, Robert Hanson wrote: > Looks like it is as simple as this: > > >var firstPARAM = "p1_b"; >var SECONDparam = "p2_b"; > >x =

Re: [Jmol-users] msCIF problems

I checked with Vaclav, and he agrees that the file is invalid. Problem #2 is with loop_ _jana_atom_site_displace_Legendre_atom_site_label _jana_atom_site_displace_Legendre_axis _jana_atom_site_displace_Legendre_param_order _jana_atom_site_displace_Legendre_param_coeff that was a bug #3 cra

Re: [Jmol-users] Mol Ready Question

On Sat, Jun 13, 2015 at 8:59 AM, Otis Rothenberger wrote: > Bob, > > Am I correct on these 2 points: > > 1) jmol_isReady() is only called when Jmol originally loads AND the first > model is loaded. > > correct: if (script.length() > 0) scriptProcessor(script, null, SCRIPT_WAIT); vi

Re: [Jmol-users] Function call with hash parameter - case conversion

Looks like it is as simple as this: var firstPARAM = "p1_b"; var SECONDparam = "p2_b"; x = ["FIRSTParam": "p1_a", secondPARAM: "p2_a"] print x giving { "FIRSTParam" : "p1_a" "secondparam" : "p2_a" } ​ Note that putting the names in quotes takes care of it. Looking into it

Re: [Jmol-users] jmol.php

Just add your server to the list of known servers that implement access-control-allow-origin: * Jmol._DirectDatabaseCalls["http://chemagic.com";] = "%URL" On Sat, Jun 13, 2015 at 8:18 PM, Otis Rothenberger wrote: > Bob, > > I have a server script that I use for loading remote files. Is there

Re: [Jmol-users] msCIF problems

well, Here's what Jana2006 says. It's invalid. Do you have that so you can do your own testing? That said, I'm not adverse to having Jmol read these. But I really think you need to divide the wave vectors by 1/2. I'll ask Vaclav about this. Bob [image: Inline image 1] On Fri, Jun 12, 201

Re: [Jmol-users] msCIF problems

will look at this as soon as possible. I'm sure it's something simple. On Fri, Jun 12, 2015 at 10:27 AM, wrote: > Just been testing Jmol 14.2.14 with my collection of msCIFs. > I am seeing a number of file reading problems (JSmol and Java application) > and a number of instances where the JSmol

Re: [Jmol-users] echo image questions

OK, a major rewrite of the image-loading method. http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.15_2015.06.12.zip Good luck, Frieda! On Thu, Jun 11, 2015 at 9:09 AM, Robert Hanson wrote: > > > On Thu, Jun 11, 2015 at 7:21 AM, Frieda Reichsman > wrote: > >> Transpa

Re: [Jmol-users] echo image questions

had fixed that. > > Thanks, > Frieda > > > On Jun 11, 2015, at 1:29 AM, Robert Hanson wrote: > > I had only tested *tranparent* PNGs, as it turns out. This is one of the > very few issues with JavaScript that I had forgotten, that > > (a & a) != a > >

[Jmol-users] Jmol 14.2.14_2015_06_11

http://sourceforge.net/projects/jmol/files/Jmol/Version%2014.2/Version%2014.2.14/Jmol-14.2.14_2015.06.11-binary.zip/download Jmol.___JmolVersion="14.2.14_2015.06.11" bug fix: polyhedra broken for number of vertices > 6. -- needed smaller default distanceFactor (set to 1.5; formerly 1.85) code:

Re: [Jmol-users] echo image questions

I had only tested *tranparent* PNGs, as it turns out. This is one of the very few issues with JavaScript that I had forgotten, that (a & a) != a in certain cases. Anyway, the various image types are working now, and I have released a new version on SourceForge -- see https://sourceforge.net/pro

Re: [Jmol-users] Capture multi-GIF from applet?

I don't plan on having capture available for the applet. On Wed, Jun 10, 2015 at 2:20 PM, Eric Martz wrote: > Hi, Bob, > > I would love to have a button in FirstGlance in Jmol that, when pushed, > would generate a spinning animation multi-gif of the current view. I > suppose this would be possib

Re: [Jmol-users] echo image questions

ase. > > Frieda > > > On Jun 10, 2015, at 8:11 AM, Robert Hanson wrote: > > yes, sorry -- I just realized that it was only transparent over the > background, not the model. > > see http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.14_2015.06.10c.zip > > removing jmol-

Re: [Jmol-users] Jmol Application Gaussian export/tool

JR Schmidt at UW Madison is working hard to create a JavaScript-only version of WebMO. I think he is making good progress, and it will probably be independent of Jmol. I believe his solution will be to use WebGL for the HTML5 version and an independent application for iOS. Don't know exactly what h

Re: [Jmol-users] echo image questions

st2 0% 0%; > set echo ~test2 image "img2.png"; // a png with transparent bkg > set echo ~test2 scale 0.2; > set echo ~test2 depth 0; > > > On 10 Jun 2015 at 1:29, Robert Hanson wrote: > > It's fixed. Thanks for pointing

Re: [Jmol-users] Jmol Application Gaussian export/tool

yes, very simple. See http://chemapps.stolaf.edu/jmol/zip/Jmol.jar On Tue, Jun 9, 2015 at 5:41 PM, Kubasik, Matt wrote: > Dear Bob, > > Sometime between 14.1.14 and 14.2.14, the application's Gaussian export > tool broke. I think the break may correspond with moving the writing of > Gaussian

Re: [Jmol-users] echo image questions

It's fixed. Thanks for pointing this out, Frieda. See http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.14_2015.06.10.zip Jmol.___JmolVersion="14.3.14_2015.06.10" bug fix: animation buttons go to wrong first frame for FRAME [3 2 1] bug fix: JSmol set echo IMAGE not working properly (Frieda Reichsm

Re: [Jmol-users] using timeout while a file is retrieved

Try load ASYNC "x" It will cause the load command to run twice -- first to start the loading and then to conclude the loading. This uses an asynchronous channel. I tried it just now with n = 0; ... xxn = setInterval(function() {document.title = "testing " + (n++);},1) and it fired up

Re: [Jmol-users] echo image questions

I doubt it is a restriction in terms of HTML5. I suspect it is a problem with the way the image is transferred. Looks like enough for me to test. I'll try to look at it tonight.​ -- _

Re: [Jmol-users] echo image questions

(read that wrong - thought it was about the image command) I will look into why that is happening. On Mon, Jun 8, 2015 at 1:35 PM, Robert Hanson wrote: > This is supposed to be the same in the app and applet. Just make sure you > also give two distinct IDs. > > image ID i1

Re: [Jmol-users] echo image questions

This is supposed to be the same in the app and applet. Just make sure you also give two distinct IDs. image ID i1 . image ID i2 or the second will simply take the place of the first. ​ -- __

Re: [Jmol-users] Set picking label - label moving problems

THAT was a very difficult bug to fix -- glad to have it done. The problem was associated with several other issues in relation to how label offsets were handled. Now that should be cleared up. see http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.14_2015.06.06.zip JmolVersion="14.3.14_2015.06.06" bu

[Jmol-users] Jmol-14.2.14_2015.06.01-binary.zip (59.1 MB)

Looking for the latest version? * Download Jmol-14.2.14_2015.06.01-binary.zip (59.1 MB) * Jmol.___JmolVersion="14.2.14_2015.06.01" bug fix: unncessary dialog with LOAD ? when using JSmol/HTML5 bug fix: write("pdb") not ret

[Jmol-users] jmol-14.3.14_2015.06.01.zip

http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.14_2015.06.01.zip Jmol.___JmolVersion="14.3.14_2015.06.01" new feature: preliminary AFLOW AaBb binary file reader - see http://www.aflowlib.org/binary_alloys.php new feature: NBO cfi file writer - print data({*}, "cfi") bug fix: draw pointgroup a

Re: [Jmol-users] Selecting specific hydrogen atoms

!_H On Mon, Jun 1, 2015 at 4:26 PM, Robert Hanson wrote: > You could also use > > display !H or backbone > > I believe. The NH hydrogens are considered backbone. > > I do not recommend *restrict*. It is totally irreversible. > > Bob > > > > ​ > --

Re: [Jmol-users] Selecting specific hydrogen atoms

You could also use display !H or backbone I believe. The NH hydrogens are considered backbone. I do not recommend *restrict*. It is totally irreversible. Bob ​ -- ___ Jmol

Re: [Jmol-users] DOCUMENTATION: capture

thanks, Eric. On Mon, Jun 1, 2015 at 1:49 PM, Eric Martz wrote: > Hi, Bob! > > This command in the manual > > capture "filename" ROCK axis degrees > > has the order of parameters reversed. It should be corrected to: > > *capture "filename" ROCK **degrees axis* > > Best regards, Eric > > > ---

Re: [Jmol-users] Code Snippet

Sorry, that was a concatenation of two ideas: This also works. load $caffeine print {*}.mass.sum 194.194​ -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net h

Re: [Jmol-users] Code Snippet

Clever! For full molecules from NCI you can also do: I think this also works. load $caffeine print {*}.mass.sum 194.194 ;) -- ___ Jmol-users mailing list Jmol-users@lists.sourc

Re: [Jmol-users] Jmol 14.2.14/14.3.14 write("xyz") misbehavior?

Yes, found that and fixed it. Will have a new version out tonight. ​ -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/j

Re: [Jmol-users] Idea for using JSmol as Wiki-Extension

I DO love it! One suggestion: Use radio buttons rather than checkboxes. It gets messy fast, and that would keep it simpler. On Thu, May 28, 2015 at 1:45 AM, Birgit Lachner wrote: > Hello to all, > > > found some weeks ago a video that explains me, who to show Atom-Orbitals > and LCAO-Orbitals

Re: [Jmol-users] Query about change from Jmol to JSmol

Your Jmol2.js is faulty. It needs to read: Jmol.Info = { // uncomment one or more of these next lines only if you want to override jmolInitialize() //jarPath: "java", //jarFile: "JmolAppletSigned0.jar", //j2sPath: "j2s", use: "HTML5", //

[Jmol-users] Jmol 14.2.14/14.3.14 released

https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.2/Version%2014.2.14/ Jmol.___JmolVersion="14.2.14_2015.05.25" release; synchronized with 14.3.14 changes since release of 14.2.13 in March: new feature: set contextDepthMax -- sets the maximum depth of contexts, including {}, if{}

Re: [Jmol-users] SwingJS proceeding as hoped

Joel, Good to hear from you! That sounds great. I don't do that sort of pathway business, but I can see that if I did, this would be the way to go. It is Java based, but there is no indication that they were able to port that directly to JavaScript. To me it sounds like they started from scratch.

Re: [Jmol-users] strange behaviour of files

Your code reads: jmolButton("load wp-content/chlorobenzene.txt;isosurface resolution 6 vdw 80% color range all map MEP translucent;", "MEP 80%vdw", "MEP 80%"); jmolButton("load wp-content/fluorobenzene.txt; isosurface resolution 6 vdw 80% color range all map MEP translucent;", "MEP 80%vdw", "MEP

Re: [Jmol-users] Evaluate Problem with 14.3.13_2015.05.12

script -- includes: historylevel;imagestate;iskiosk;useminimizationthread; -- includes: showkeystrokes;saveproteinstructurestate;testflag1;testflag2;testflag3;testflag4 On Wed, May 13, 2015 at 10:42 PM, Robert Hanson wrote: > it is deprecated; you should use > > Jmol.evaluateVar() > >

Re: [Jmol-users] Evaluate Problem with 14.3.13_2015.05.12

it is deprecated; you should use Jmol.evaluateVar() but it may be broken as well. :( On Wed, May 13, 2015 at 8:37 PM, Otis Rothenberger wrote: > It seems to be Jmol.evaluate() in general. Did I miss something? Is that, > indeed, deprecated? > > Otis > > > > On May 13, 2015, at 9:27 PM, Otis R

Re: [Jmol-users] jmol-14.3.13_2015.05.12.zip

Rolf, is this JavaScript or Java you are using? If JavaScript, you can experiment some by replacing 100==this.scriptLevel&&this.error(44); in jsmol/j2s/core/corescript.z.js with a number greater than 100. Bob ​ -- One

[Jmol-users] jmol-14.3.13_2015.05.12.zip

http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.13_2015.05.12.zip Jmol.___JmolVersion="14.3.13_2015.05.12" bug fix: re-entering functions loses if/else state bug fix: more issues with low-resolution linear-z index lines. Need to compromise for isosurfaces and nucleic cartoons --

Re: [Jmol-users] Jmol 14.3.13_2015.05.08

n > every double click. > > Otis > > > On May 12, 2015, at 2:21 PM, Robert Hanson wrote: > > Wait. > > Maybe that 08 zip file got messed up. > > 1) You really DO need 05.08. > 2) The chemapps site applet DOES report 05.08 > 3) The Java.jar application in that zip f

Re: [Jmol-users] Jmol 14.3.13_2015.05.08

(for me). Bob On Tue, May 12, 2015 at 1:15 PM, Robert Hanson wrote: > So what's the scoop then on that issue? > > Is it only an issue with your Mac? > Anyone else having this problem? > > At http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm > > I opened the

Re: [Jmol-users] Jmol 14.3.13_2015.05.08

So what's the scoop then on that issue? Is it only an issue with your Mac? Anyone else having this problem? At http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm I opened the Jmol console and clipped this into the input box and pressed RUN and it works fine: set picking dragMolecule bind "left-do

Re: [Jmol-users] Recursive functions allowed?

Oh, I see. yes, that looks like a bug. You mean, it should only report one "recursion finished at level..." Now I get it. On Tue, May 12, 2015 at 9:51 AM, Rolf Huehne wrote: > On 05/12/2015 04:36 PM, Robert Hanson wrote: > > Hmm, this looks good to me: > &g

Re: [Jmol-users] Version Confusion

Every once in a while I forget to update the flag inside the file; it's not 100% automated. OK, well, then you have the latest. It should work. There's also a newer one already. On Tue, May 12, 2015 at 10:47 AM, Otis Rothenberger wrote: > Bob, > > I guess I’m being a little dense on JSmol versi

[Jmol-users] SwingJS proceeding as hoped

Jmol Developers, and friends of Jmol, I will use this as an opportunity to pitch my latest project, which is *not *Jmol: SwingJS. http://sourceforge.net/projects/swingjs/ The objective of this project is to have a "universal" applet Java-to-JavaScript conversion, allowing drop-in of working Swin

Re: [Jmol-users] structured callback

Good to see that is working for you, Dan. Hooray! You guys are doing great work. ​ Bob -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applicat

Re: [Jmol-users] Curious 3A bond between sulfurs

Here's your problem: CONECT10280 411610264 select on @10264,@10280,@4116 ​[image: Inline image 1] -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with

Re: [Jmol-users] Recursive functions allowed?

Hmm, this looks good to me: show functions /* * rectest */ function rectest (level){ print "level="+ level +" maxLevel=" + maxLevel + "\n"; if (level < maxLevel) { print "recursing at level " + level+"\n"; recTest(level + 1); } else { print "recursion finished at level

Re: [Jmol-users] Jmol 14.3.13_2015.05.08

Otis, please use the stated version of Jmol in the first message in this thread. That page use 05.07. Jmol.___JmolVersion="14.3.13_2015.05.08" *bug fix: BIND can cause fault* ​ -- One dashboard for servers and applicat

Re: [Jmol-users] Jmol 14.3.13_2015.05.08

Try the same thing using http://chemapps.stolaf.edu/jmol/jsmol/test2.htm This won't load core.z.js, so it might make that more understandable. How very odd. You think this message comes when you double-click? Any yet it "works"? On Sun, May 10, 2015 at 7:45 PM, Otis Rothenberger wrote: > Bob

Re: [Jmol-users] Jmol 14.3.13_2015.05.08

(I had not updated JSmol on chemapps for a while, so it wouldn't work there anyway until just now when I updated it. Sorry to imply that it should. So, anyway, sounds like that is either a Mac problem or a version problem.) On Sun, May 10, 2015 at 12:39 PM, Robert Hanson wrote: > Can yo

Re: [Jmol-users] Jmol 14.3.13_2015.05.08

ragAtom;background yellow;bind 'left-drag' _rotateSelected ;set allowRotateSelected;}" On Sun, May 10, 2015 at 6:28 PM, Robert Hanson wrote: > I definitely tried this on the distribution locally before zipping it up. > I will try again. Does sound like a version problem. Pr

Re: [Jmol-users] Jmol 14.3.13_2015.05.08

havior at > > http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm > > including Javascript console error on double click. > > Otis > > > > On May 10, 2015, at 1:39 PM, Robert Hanson wrote: > > Can you verify that this fails for you also on my site? > > On Sat,

Re: [Jmol-users] Jmol 14.3.13_2015.05.08

min.js, line 92) > handle (JSmol.min.js, line 85) > > > > On May 9, 2015, at 11:56 AM, Robert Hanson wrote: > > Shouldn't be any difference on a Mac. Left is Left. (I guess Alt may not > be Alt) > > From the jsmol site directory you unzipped, start jsmol.htm,

Re: [Jmol-users] Jmol 14.3.13_2015.05.08

er than normal axis rotation. > > Otis > > On May 8, 2015, at 11:11 PM, Robert Hanson wrote: > > > > On Fri, May 8, 2015 at 1:33 PM, Otis Rothenberger > wrote: > >> Thanks Bob, but I’m still having problems. This may relate the approach >> that I’m using t

Re: [Jmol-users] Jmol 14.3.13_2015.05.08

On Fri, May 8, 2015 at 1:33 PM, Otis Rothenberger wrote: > Thanks Bob, but I’m still having problems. This may relate the approach > that I’m using that worked in the past. In this approach, I use the screen > as two of your buttons - i.e. double tap screen to toggle rotate translate > modes. In

Re: [Jmol-users] Adjust backbone thickness

depends what you mean by "per residue." Backbone lines are from C-alpha to C-alpha. We don't have a way to go half way from one to the next with different line widths. But if you mean different segments with different lengths, sure. No problem. Just select both ends: select 1,2 backbone 0.2 select

[Jmol-users] Jmol 14.3.13_2015.05.08

http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.13_2015.05.08.zip Jmol.___JmolVersion="14.3.13_2015.05.08" bug fix: BIND can cause crash bug fix: set picking dragMolecule, set picking dragMinimizeMolecule, set picking dragLigand broken bug fix: write "?" can cause crash when [x] box is pushed on

Re: [Jmol-users] Drag

I have three molecules in the window, the approach below requires > exclusive selection of the clicked model to be dragselected? > > This is not a big deal, but dragmolecule covered you on this point, which > was a convenience. Nevertheless, if the answer to 1 and 2 is “correct” and > “y

Re: [Jmol-users] Drag

Otis, I think what you want is: left-drag --> move atoms *set picking dragselected* left-drag --> rotate molecule *set allowrotateselectedunbind "_dragAtom" // was left+dragunbind "_rotateSelected" // was alt+left+dragbind "left+drag" _rotateSelected // now left+drag* clear all t

[Jmol-users] jmol-14.3.13_2015.05.07.zip

http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.13_2015.05.07.zip Jmol.___JmolVersion="14.3.13_2015.05.07" bug fix: isolated bio groups such as AMP, which are not part of biopolymers, can result in crashes when colored or queried about their parameters (Hiroufmi Suzuki) bug fix: new SQL *

Re: [Jmol-users] How to select atoms outside of a regional?

Max, That is exactly how you do it. So I am guessing that you have one or more of your planes defined backwards. Winding is important here. Test your planes one at a time and try +/-20 in each case. Once you have each plane working, it should work. It is convenient to use the ON keyword here so

Re: [Jmol-users] SQL syntax for two-dimensional associative arrays

Ah, yes! I see that. Fixed. Standby... On Thu, May 7, 2015 at 5:16 AM, Rolf Huehne wrote: > On 05/07/2015 05:11 AM, Robert Hanson wrote: > > Jmol.___JmolVersion="14.3.13_2015.05.06" > > > > http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.13_2015.05.06.zip >

Re: [Jmol-users] freeze by "color monomer"

Indeed. Thank for this, Hiroufmi. I will upload a version with that fix to http://chemapps.stolaf.edu/jmol/zip later today. On Thu, May 7, 2015 at 5:41 AM, Hiroufmi Suzuki wrote: > Hi All > > Jmol freezes by this command. > load "http://www.rcsb.org/pdb/files/2WEF.cif.gz";; color monomer;

Re: [Jmol-users] is structureModifiedCallback working?

JmolVersion="14.3.13_2015.05.05" bug fix: set structureModifiedCallback does not work with "JmolScript:" http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.13_2015.05.06.zip -- One dashboard for servers and applications ac

Re: [Jmol-users] SQL syntax for two-dimensional associative arrays

Jmol.___JmolVersion="14.3.13_2015.05.06" http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.13_2015.05.06.zip new feature: "drilling" in associative arrays for sub arrays with a given property (Rolf Huehne) -- uses "**" as the SELECT option, sort of the way ** sometimes means "subdirectories of"

Re: [Jmol-users] is structureModifiedCallback working?

It's a bug in that although this works with JavaScript and the applet, I forgot to add the line of code that allows it to be captured with set structureModifiedCallback "jmolScript:" ​Bob -- One dashboard for servers

[Jmol-users] jmol-14.3.13_2015.04.29.zip

Jmol.___JmolVersion="14.3.13_2015.04.29" bug fix: perspective renderer was using the wrong formula for calculating Z depth of pixels: * Well, it turns out that the calculation of the intermediate pixel z value * in all methods involving rasterization of lines is incorrect and has been * incorr

Re: [Jmol-users] Dragging only selected atoms

Definitely Wikipedia. http://en.wikipedia.org/wiki/Wikipedia:Manual_of_Style#Wikilinks On Wed, Apr 29, 2015 at 7:25 AM, Rolf Huehne wrote: > On 04/28/2015 10:25 PM, Robert Hanson wrote: > > Feel free to adjust - General wiki style, I think, is to provide links > once > > but

Re: [Jmol-users] Dragging only selected atoms

hiding the essential information -- that really it is just one or two very specific settings that do each of these. It was a good exercise for me to work on this, because it pointed out some oddities in that logic. On Tue, Apr 28, 2015 at 6:29 AM, Rolf Huehne wrote: > On 04/27/2015 09:02 PM,

Re: [Jmol-users] Dragging only selected atoms

I did some more editing --- hope it is not too much. http://wiki.jmol.org/index.php/Mouse_Manual#Additional_options On Mon, Apr 27, 2015 at 2:02 PM, Robert Hanson wrote: > Rolf, how does that look? Do you think there might be other "specific > cases" we could highlight in th

Re: [Jmol-users] Dragging only selected atoms

on, Apr 27, 2015 at 8:21 AM, Rolf Huehne wrote: > On 04/27/2015 02:40 PM, Robert Hanson wrote: > > OK, I added some text there. Feel free to edit. > > > The crosslinks are corrected now. > > Regards, > Rolf > -- > > Rolf Huehne > Postdoc > > Leibniz In

Re: [Jmol-users] Dragging only selected atoms

OK, I added some text there. Feel free to edit. On Mon, Apr 27, 2015 at 6:35 AM, Robert Hanson wrote: > That is really complicated, isn't it? > > Rolf, I'm working on the page a bit to add a header section, so please > don't change it for 30 minutes or so. But when I

Re: [Jmol-users] Dragging only selected atoms

015 at 5:24 AM, Rolf Huehne wrote: > On 04/24/2015 05:29 PM, Robert Hanson wrote: > > It's pretty much a nightmare. Maybe you could get that on the Wiki. > > > I have added it as the new section 'How to change atom coordinates' to > the english version of t

Re: [Jmol-users] Dragging only selected atoms

It's pretty much a nightmare. Maybe you could get that on the Wiki. On Thu, Apr 23, 2015 at 12:37 PM, Rolf Huehne wrote: > On 04/23/2015 02:20 AM, Robert Hanson wrote: > > The missing info is that you need > > > > > > > > * set picking DRAGSELECTED se

Re: [Jmol-users] Dragging only selected atoms

The missing info is that you need * set picking DRAGSELECTED set allowMoveAtoms TRUE* in order to move subsets of atoms in a molecule along with * set allowRotateSelected TRUE* if you want to also rotate them with alt-left I've just spent some time looking closely at the difference betwe

Re: [Jmol-users] Dragging only selected atoms

It´s quite confusing from the documentation, and I´m not certain that overall the logic is sound. You need *set picking dragAtom* if that´s what you want to do. *set picking dragSelected* by itself allows dragging of *full molecules* associated with the currently selected atoms set drags al

Re: [Jmol-users] mmCIF - higher numbers refused as chain ids

misplaced line of code. On Wed, Apr 22, 2015 at 12:29 AM, Robert Hanson wrote: > OK, that should be good enough to go by. I agree about matching the CONECT > records with mmCIF data. That's important. > > On Tue, Apr 21, 2015 at 6:00 AM, Rolf Huehne > wrote: > >>

Re: [Jmol-users] mmCIF - higher numbers refused as chain ids

OK, that should be good enough to go by. I agree about matching the CONECT records with mmCIF data. That's important. On Tue, Apr 21, 2015 at 6:00 AM, Rolf Huehne wrote: > On 04/20/2015 10:29 PM, Rolf Huehne wrote: > > Am 20.04.15 um 20:25 schrieb Robert Hanson: > >&g

Re: [Jmol-users] mmCIF - higher numbers refused as chain ids

Bob On Mon, Apr 20, 2015 at 8:44 AM, Robert Hanson wrote: > how unusual! I will look into it. Definitely a bug. I can't imagine why it > is doing that > > On Mon, Apr 20, 2015 at 8:42 AM, Rolf Huehne > wrote: > >> Hi all, >> >> the mmCIF format ge

Re: [Jmol-users] mmCIF - higher numbers refused as chain ids

how unusual! I will look into it. Definitely a bug. I can't imagine why it is doing that On Mon, Apr 20, 2015 at 8:42 AM, Rolf Huehne wrote: > Hi all, > > the mmCIF format generally allows multicharacter chain ids. This should > also include numeric characters. > But Jmol 14.3.13_2015.04.17

Re: [Jmol-users] boundbox, unitcell and Tinker arc files

On Tue, Apr 14, 2015 at 8:01 PM, Whitwell, George wrote: > Greetings, > > > > The first two items developed while working with Tinker 6 output. > > > > *boundbox* > > I am loading Tinker 6 molecular dynamics arc files (which are catenated > Tinker xyz files) that were the result of an NPT dynami

Re: [Jmol-users] Echo displays ID insetead of echo text

ps. If you set loglevel 3 this turns off the echo reporting. On Thu, Apr 9, 2015 at 2:01 PM, Robert Hanson wrote: > I guess the developer would know something about the context of the > messages. If they are hidden, you can make them anything you want, of > course. The messaging

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