[Jmol-users] SMARTS question

This selects the aromatic ring carbons of Phe and Tyr: rings6 = {*}.find("SMARTS","c1c1", true) It does not select the 6-atom ring of Trp. This selects the ring of His: ringsh = {*}.find("SMARTS","c1cncn1", true) How do I select the 5 and 6 atom rings of Trp? Thanks, Eric

Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

Hi, Henry, In addition to Internet Explorer 11* (still included in Windows 10 as far as I know), several minor browsers that still supported Java when last I checked in March 2017 are listed here: http://proteopedia.org/w/Installing_and_enabling_Java#Browsers_That_Support_Java * See

Re: [Jmol-users] Jmol Anniversaries?

Hi Henry, I have a paragraph of Jmol history in footnote 1 here: http://proteopedia.org/w/Jmol Which leads to early history by searching for "jmol" at openscience.org: http://openscience.org/?s=jmol Much of Jmol's command language was invented by Roger Sayle when he created RasMol. Tim

Re: [Jmol-users] labeling residue by position relative to observer

Dear Luciano, Wow! That is amazing! It worked easily for me (MacBook Pro). For people who haven't tried it: Go the link below. It asks permission to use your camera. Follow simple instructions to calibrate (takes less than one minute). Then whatever part of the molecule you look at rotates

Re: [Jmol-users] labeling residue by position relative to observer

-- as far as I know, this method has not yet been incorporated into Molecular Playground modules, or any other uses. -- // orient.spt -- tracks the orientation of four points // This script by Robert Hanson, April, 2012 for Karsten Theis, Eric Martz, Craig Martin

Re: [Jmol-users] ...still problems with the extended display...

Did you try moving the console to where you want it, then clicking Quit (or Close) from Jmol's pull-down File menu? On a Mac, this saves the window positions so the next time you start Jmol, they are remembered. In contrast, other methods of quitting (Jmol menu in the menubar, Quit; Cmd-Q) do

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,

Re: [Jmol-users] Java support in browsers

Correction: On 4/6/17 5:58 PM, Eric Martz wrote: > Windows 10: Firefox ESR, Pale Moon, Seamonkey, Maxthon (but see > caution about data sent to China by Maxthon at above link). I can't > test Waterfox because I don't have 64-bit Windows. The correction is that Firefox ESR in Windows

Re: [Jmol-users] Java support in browsers

Thanks, Henry! I did not know about unchecking "Run in safe mode" (hidden unless you hold down the option key). After doing that, I can run Jmol_S Java applet from local files (FirstGlance in Jmol) in Safari, which is convenient for testing while developing. We list browsers that still

Re: [Jmol-users] rotate best? DOCUMENTATION

d to me to select all first. Also I had difficulty understanding "thinnest along the line of site". (It should be "line of sight"). I suggest "thinnest front to back". Jean-Baptiste: do "select all" before you "rotate best". Bob: Thanks! -Eric

[Jmol-users] rotate best?

1. When I apply "rotate best" to 1d66, I expect the distance from the frontmost to backmost atoms to be minimized, and the distance from the leftmost to rightmost atoms to be maximized. Neither appears to happen. Do I misunderstand the goal? " Rotates the model to a calculated "best"

[Jmol-users] Protein sequence alignment display/analysis: MSAReveal.Org

, and with alignments containing hundreds of sequences. Sincerely, Eric -- Eric Martz, Professor Emeritus, Dept Microbiology University of Massachusetts, Amherst MA US Martz.MolviZ.Org <http://Martz.MolviZ.

Re: [Jmol-users] Java Applet Mouse problems in Firefox on MacOS 10.11.6

Tested on OS 10.10.5 Yosemite, Java 1.8.0_101: Jmol.jar: wheel zoom and 2 of the 3 mouse translation modes work. I can't get double click of wheel and drag to work but it might relate to some configuration of the wheel click on my system. Rolf said the mouse gestures work in the application.

Re: [Jmol-users] Java Applet Mouse problems in Firefox on MacOS 10.11.6

Dear Rolf, I confirm the failure of translation by mouse (all 3 methods) in Firefox with Java, and the failure of wheel zoom in Firefox or Safari (but yes translation is working in Safari+Java). However, I tested in OS 10.10.5 *Yosemite*, with Java 1.8.0_*101*, Firefox 49.0, Safari *10.0*.

Re: [Jmol-users] Java Applet Mouse problems in Firefox on MacOS 10.11.6

Correction to my previous message: On the Mac Mini I have NOT upgraded Java to 101. Those test results were with Java 1.8.0_*91*. -Eric -- ___ Jmol-users mailing list

[Jmol-users] Crash attempting a compare

Dear Bob, I did an alignment using compare between two PDB files and it worked perfectly. I attempted a very similar one and Jmol (July 11) freezes. Easy to reproduce: https://www.dropbox.com/s/q71q3vfdszyru9c/myosin_morph_Eric.zip?dl=0 Run the Jmol.jar in that folder (as file references are

[Jmol-users] show 1-letter sequence?

How do I show the one-letter amino acid sequence? (without the sequence numbers, e.g. ready for a BLAST search) I see 'show sequence' which reports 3-letter amino acid codes with sequence number. I looked at 'getProperty' but did not spot what I need. Thanks, Eric

[Jmol-users] Write 2 PDB models?

If I load 2 models, then "frame all; select all;", I expect that "write PDB" will write both models. Instead, the PDB file has MODEL/ENDMDL records for 2 models, but the first model contains no coordinates. Is this a bug or a feature? load =3hyd load append =4qxx frame all select all write

Re: [Jmol-users] Rename chain?

Interesting idea, Angel. But part of my purpose is to be able to create crystal symmetry PDB files that can be handled by FirstGlance as it is. It assumes that each chain has a different name and many of its tools are coded under that assumption. With all the other power in Jmol, it seems

Re: [Jmol-users] Rename chain?

, Jun 19, 2016 at 8:43 PM, Eric Martz <ema...@microbio.umass.edu <mailto:ema...@microbio.umass.edu>> wrote: How do I change the name of a chain from e.g. A to B? For example, I load chain A, then load append the same chain A, then translate selected 2.1. I would

[Jmol-users] Rename chain?

How do I change the name of a chain from e.g. A to B? For example, I load chain A, then load append the same chain A, then translate selected 2.1. I would rather refer to the translated chain as chain=B than (chain=A and 2.1). (This is a simple example but the actual case I have in mind has

Re: [Jmol-users] updating SpectralZoo pages

New versions of JSmol are supposed to be backwards compatible. There are very few intentional changes that require changes in the JSmol command scripts, generally quite minor. It would be good to "set debugscript on" and see where the errors occur. If you are still stumped, copy the error

[Jmol-users] A little history

John Keller University of Alaska Fairbanks Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 *From: *Eric Martz <mailto:ema...@microbio.umass.edu> *Sent: *Wednesday, June 1, 2016 1:25 PM *To: *jmol-users@lists.sourceforge.net <mailto:jmol-users@lists

Re: [Jmol-users] Jmol for mac installation

Dear John, Jmol, by itself, is challenging to use for most purposes. It has an extensive command language with thousands of commands and permutations. Therefore many people, myself included, have created explanations or tutorials that show molecules using Jmol, but are much easier to use,

[Jmol-users] Animations from FirstGlance in Jmol

I have just released a new version of FirstGlance in Jmol with the ability to save static images or presentation-ready multi-GIF animations. I have tried to make a user-friendly interface that can save these in just a few clicks, with optimal defaults. I welcome

Re: [Jmol-users] Hide unitcell text?

Thank you Angel! That works! -Eric On 5/30/16 5:52 AM, Angel Herráez wrote: > Dear Eric > I think it's this: > > set displayCellParameters false > > > > -- > What NetFlow Analyzer can do for you? Monitors network

[Jmol-users] Hide unitcell text?

I use load "" {555 555 1} range -7.0; to show crystal contacts. That command automatically displays unit cell parameters and space group as text in the upper left corner of Jmol. It looks like an echo but set echo off does not hide it. I would appreciate some way to hide/display that text.

Re: [Jmol-users] capture hermitelevel full quality

That works! Thanks Bob and Angel! On 5/27/16 1:39 AM, Robert Hanson wrote: sure enough -- I forgot about that: int val1 = vwr.getHermiteLevel(); val1 = (val1 <= 0 ? -val1 : vwr.getInMotion(true) ? 0 : val1); Thus, hermite level is set to 0 only if the value is positive and the model

Re: [Jmol-users] capture hermitelevel full quality

Dear Angel, No I was NOT aware of the minus trick for hermitelevel. Indeed, that preserves full quality during mouse rotation, but not during capture. Bob: perhaps all that is needed then is to extend the minus hermitelevel trick to the capture command. Thanks Angel! -Eric On 5/26/16 2:19

[Jmol-users] capture hermitelevel full quality

Dear Bob, I would like to request a new setting that enables multi-GIFs captured for presentations to show the full beauty of non-zero hermitelevels, antialiased. Currently, rendering is simplified (even at platformSpeed 10) during rotation. This is good. But when using "capture", speed is

Re: [Jmol-users] hermiteLevel vs. cartoon bug

Thank you Bob. The May 24 version seems to work as desired regarding hermitelevel. Also in comparing, I noticed that with hermitelevel on in the May 17 version, at high zoom, JSmol essentially freezes when you try to rotate. The May 24 version rotates at reasonable speed, even with

Re: [Jmol-users] jmolScriptWait() vs. symmetry loading

OK thanks for the heads up! On 5/24/16 9:27 PM, Robert Hanson wrote: Eric, I do see that it takes an oddly long time to load a file using scriptWait (5 seconds instead of instantaneously). I don't know what that is about, but it suggests you should not use scriptWait for loading a file, if

[Jmol-users] jmolScriptWait() vs. symmetry loading

This is merely FYI: When sent with jmolScript*Wait*(), the following commands work in JSmol/HTML5 but not in Jmol_S/Java: load "" {555 555 1} range -7.0; # loads asymmetric unit plus crystal contacts within 7.0 Angstroms load "" {1 1 1}; # loads unit cell They work fine in Jmol_S/Java when

[Jmol-users] Unit cell, axes bug/feature?

Dear Bob, In JSmol December 23 2015 (and earlier) the following commands do NOT display the unit cell nor axes: load "" {555 555 1} range -7.0; load "" {1 1 1}; In JSmol May 17, 2016 these commands display the unit cell and axes. Is this an intentional change? Its easy enough to turn the

Re: [Jmol-users] Jmol_S crash by set picking center in FirstGlance only

Dear Bob, Thanks for pointing me to investigate pickCallBack. The problem was that clicking an atom in "set picking center" mode was sending, via pickCallBack, an otherwise innocuous script via jmolScript*Wait*(). This crashed the Java applet but created no problem for JSmol/HTML5. Once I

[Jmol-users] hermiteLevel vs. cartoon bug

Dear Bob, I think there is a bug regarding hermiteLevel vs. cartoon. In the May 17 (or Feb 18) application: print hermitelevel # reports default zero load =4qxx cartoon only # now I see a "rope" as expected set hermitelevel 4 # rope turns to flat rendering with elbows when rotated set

[Jmol-users] platformSpeed DOCUMENTATION

I am confused about platformSpeed. 1. Documentation says maximum value is 8, but default value is 10 since earlier than last December. 2. Does JSmol do any automatic detection of the platform and set platformspeed to lower values on e.g. mobile devices? Bob, could you please update the docs?

Re: [Jmol-users] measure label flapping

. On Sun, May 22, 2016 at 2:53 PM, Eric Martz <ema...@microbio.umass.edu <mailto:ema...@microbio.umass.edu>> wrote: The flapping of labels on angle measures also occurs in Jmol April 22 and December 23. It would be especially annoying in a captured spin or rocking

[Jmol-users] Jmol_S crash by set picking center in FirstGlance only

Dear Bob, I have run out of ideas for debugging the following problem. Perhaps you can help? After I start FirstGlance using Java http://bioinformatics.org/firstglance/fgij/fg.htm?mol=1d66 if I open the Jmol Console and enter *set picking center* and then *c**lick on an atom*, Jmol_S

Re: [Jmol-users] measure label flapping

The flapping of labels on angle measures also occurs in Jmol April 22 and December 23. It would be especially annoying in a captured spin or rocking multi-gif. On 5/22/16 3:48 PM, Eric Martz wrote: > In Jmol May 17, the labels on angles "flap" during rotation. > >

[Jmol-users] measure label flapping

In Jmol May 17, the labels on angles "flap" during rotation. I did not compare with earlier versions of Jmol. Demo: At http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm (Is there a way to specify an earlier Jmol version here?) With caffeine in the reset position measure 14 5 2 now turn on

Re: [Jmol-users] JmolApplet.jar

Dear Bob, 1. Is JmolApplet.jar the /unsigned/ applet? I don't mind dropping that from the distribution. 2. JSmol/HTML5 is truly a life-saver! Bless you Bob and the other team members for JSmol! For most entries in the PDB, it is perfectly satisfactory and it is the default in

[Jmol-users] DOCUMENTATION set echo

Dear Bob, Under "set echo" section "scaling" Is a red link to "set fontScaling true" but the link incorrectly goes to "#setmisc". It should go to "#setlabels". Thanks, Eric -- Find and fix application performance

[Jmol-users] Message/print echo text?

Is there a way to message or print (or show) the text currently displayed at a named echo position? For example, something like set echo top left echo "1d66" message echo top but that message command doesn't work and I haven't found a method. Of course I can keep what I echo in a

[Jmol-users] request: slabByAtom false for "slab set"

Dear Bob, "slab set" will be very useful to convey to novices what "slab on" is doing. It would be more useful if the cut face would remain flat (cutting through some atoms) rather than removing cut atoms, leaving only spherical atoms inside the cut plane. That is, could "set slabByAtom

[Jmol-users] capture resets slab :(

"capture" appears to reset slab. This is frustrating since I was anticipating a marvelous animation showing the internal cavity of a proteasome (rocking). Tested with Valentine's Day Jmol app. load =1d66 slab 50 slab on slab set capture "x.gif" rock 45 -Eric

[Jmol-users] slab vs. visible?

$ load =1d66 select all # FIRST SELECT slab 50 depth 50 slab on slab set depth set select visible # SECOND SELECT TRANSCRIPTION/DNA 06-MAR-92 1D66 DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX found biomolecule 1: D, E, A, B 1D66 1762 atoms selected 1762 atoms selected # I was

[Jmol-users] cyclic peptide trace?

1hvz is a cyclic 18 amino acid peptide with a peptide bond between residues 1 and 18. JSmol shows a break in the cartoon/trace/backbone between 1 and 18, but in wireframe, shows the peptide bond. Is the break in cartoon/trace/backbone a bug or a feature? -Eric

Re: [Jmol-users] Mouse-slabbing in JSmol on Mac

In FirstGlance, I changed the key binding for dragging the entire slab with this Jmol command: bind "ALT+SHIFT+LEFT+drag" _slabAndDepth; The help panel that appears when you depress the Slab button in FirstGlance includes *"Drag the slab*: hold down ALT and SHIFT, then click and drag up and

[Jmol-users] make isomesh lines closer?

The script below generates isomeshes that look like this: Is there some way to make the lines in the isomesh closer together (more lines per Angstrom), or the sizes of triangles/squares in solid surfaces smaller? (This is what we thought 'resolution' might have done.) BEGIN SCRIPT zap

[Jmol-users] Electron Density Maps Made Easy

If you ever need a non-technical explanation of electron density maps and their relationships to temperature (B value), these pages may be quite useful: http://bioinformatics.org/molvis/edm I use them in the workshops I teach on protein structure. In 2010, with Bob's help, I made these two

[Jmol-users] Split: Websites Using Jmol

ial and agreeable change. Sincerely, Eric -- Eric Martz, Professor Emeritus, Dept Microbiology University of Massachusetts, Amherst MA US Martz.MolviZ.Org <http://Martz.MolviZ.Org> -- Site24x7 APM Insight: Get Deep V

[Jmol-users] DOCUMENTATION capture

Bob, please correct this capture "filename" ROCK degrees axis to this capture "filename" ROCK *axis degrees *Thanks, Eric* * -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM

[Jmol-users] write x.png: frank gone

The command write x.png saves the image but when saved from a browser, the orange JSmol and red Jmol_S franks are not in the image. Is there a setting to permit the frank to remain in the image? When saved from the application, the gray "Jmol" frank remains in the image. (I have tested JSmol

Re: [Jmol-users] Average of two XYZ coordinate sets?

Thank you Rolf! Wow, I thought it would be much simpler! Something like z = {x, y}.average or z = average({x}, {y}) I was sure I was missing something simple. I would never have figured this out without your help! -Eric On 1/16/16 8:31 PM, Rolf Huehne wrote: > Am 17.01.16 um 00:23 schrieb E

[Jmol-users] Average of two XYZ coordinate sets?

x = {gly6:a}.xyz y = {asp13:a}.xyz How do I get one set of XYZ coordinates that is the average of x and y? Thanks, Eric -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM:

[Jmol-users] Future of write, capture from browser?

Dear Bob and Jmol development team, You have made no comment to the contrary, so unless I hear otherwise I am going to proceed developing code for FirstGlance that assumes there is no plan to block 'write' and 'capture' operations in JSmol/HTML5 or Jmol_S/Java. Currently they do work (in some

Re: [Jmol-users] Saving files from JSmol

Dear Bob, I have updated the JSmol in my graphics saving test http://bioinformatics.org/firstglance/fgix/ to your January 9 update. When using *Java*: clicking "Save Image or Animation for Powerpoint" and then the button "Save Image": I believe that the Jmol java applet is generating this

Re: [Jmol-users] how to parse JSON data within Jmol

Dear Angel (and everyone), For years I have wanted a way to find out (in javascript or in JSmol) the number of atoms (or molecular weight) of a PDB entry before attempting to load it into JSmol. But I have not known how to do this. If you know, please send me a sample of the code. When the

Re: [Jmol-users] how to parse JSON data within Jmol

Rothenberger wrote: > Eric, > > alert(Jmol.evaluateVar(jmolApplet0, "{*}.size”)) > > should do the trick. > > Otis > -- > Otis Rothenberger > o...@chemagic.org > http://chemagic.org > >> On Jan 13, 2016, at 1:37 PM, Eric Martz <ema...@microbi

Re: [Jmol-users] how to parse JSON data within Jmol

That looks wonderful, Rolf. I'll let you know after I try it. Thanks so much!! -Eric On 1/13/16 2:28 PM, Rolf Huehne wrote: > On 01/13/2016 08:22 PM, Rolf Huehne wrote: >> On 01/13/2016 07:37 PM, Eric Martz wrote: >>> Dear Angel (and everyone), >>> >>> For y

Re: [Jmol-users] Saving files from JSmol

Dear Bob, Here is where you can test saving images or animations from a form button in FirstGlance: http://bioinformatics.org/firstglance/fgix/ You can start it with JSmol or Jmol_S (see checkbox "use Java"). Click on the orange link below the molecule "Save Image or Animation for

[Jmol-users] Saving files from JSmol

Dear Bob, It will be absolutely fantabulous if users of FirstGlance can save images and animations of the current view easily. Those animations (from the capture command) are gorgeous and attention-grabbing in Powerpoint slides. With JSmol 14.4.1_2015.12.23, I have begun writing code in

[Jmol-users] FirstGlance with 14.4.1_2015.12.23

I have released a new version of FirstGlance in Jmol that uses Jmol 14.4.1_2015.12.23. So far I have found no problems in that version of Jmol that affect FirstGlance. http://FirstGlance.Jmol.Org I have tested browsers: Firefox (best for JSmol!) in OS X and Windows Safari in OS X Chrome in OS

[Jmol-users] Chrome bug? JU.Point3fi.set2

Dear Bob, Proteopedia is attempting to use 14.4.1_2015.12.23 The following error occurs in Chrome, but not in Firefox. This occurs on all pages, e.g. this random PDB entry http://proteopedia.org/w/1ao5 This error does not occur when loading the same 1ao5 at

Re: [Jmol-users] more tests

Dear Bob, Hooray! I no longer see the 'color dots none' bug, and the one-minute freeze that I've been getting for 7ahl in FirstGlance is GONE! So far my tests in FirstGlance reveal no other bugs. Excellent work, my friend! Enjoy some time with your family! Eric On 12/23/15 4:05 AM, Robert

[Jmol-users] Bug in 12/21 build?

Hi Bob, The good news is that the 12/21 build almost passed all my tests in FirstGlance. Incidentally, while JSmol reports itself as 14.*4*.1_2015.12.*21*, Jmol_S reports itself as 14.*5*.1_2015.12.*16*. So far I only noticed one place that both JSmol and Jmol_S hiccup. It only happens

[Jmol-users] JSmol speed vs. browsers

I have provided data, methods and detailed conclusions here *http://proteopedia.org/w/JSmol/Rotation_Speeds* Briefly I found: For JSmol (HTML5/javascript) Firefox outperforms Chrome, Opera and Edge by about four-fold. Safari is as fast as Firefox with JSmol. Internet Explorer 11 is unusably

Re: [Jmol-users] Let's try this one: Jmol-14.4.1_2015.12.15

Excellent! JSmol/HTML5 appears to rotate acceptably in Chrome (still rotates more smoothly in Firefox), and Java works. Preliminary tests with FirstGlance have revealed no bugs or issues. I have replaced the jsmol in FirstGlance.Jmol.Org with the December 15 jsmol. Thanks so much Bob!!!

Re: [Jmol-users] JSmol 14.4.1 - Javascript error messages in Firefox 42

Rolf, Bob and everyone, I, too, have noticed these numerous error messages in Firefox when running from local files in OS X. Since everything seemed to work, I didn't worry about them much. But it would be nice to eliminate them so it would be easier to find the errors that matter. Thanks,

[Jmol-users] "labels off" freezing JSmol

Dear Bob, This request could be titled "another conundrum" or "a holiday puzzle for Bob" or "how about another miracle, Bob?". With the recent changes affecting rotation in Chrome, and despite your miraculous save, Firefox now outperforms Chrome for JSmol/HTML5 in every area, except one quite

[Jmol-users] 14.4.0 vs 14.4.1 and Java

Yesterday I put Jsmol 14.4.1_2015.12.13 into the public version of http://FirstGlance.Jmol.Org. This enabled use of JSmol/HTML5 with Chrome. Today I got around to trying Java. It does not work. In both Windows and OS X, the error message is "Application Blocked. Click for details. User has

Re: [Jmol-users] 14.4.0 vs 14.4.1 and Java

is temporarily more important than Java. Eric On 12/15/15 5:46 PM, Robert Hanson wrote: difference should be just the Chrome issue in JavaScript, but I guess I messed up. On Tue, Dec 15, 2015 at 2:41 PM, Eric Martz <ema...@microbio.umass.edu <mailto:ema...@microbio.umass.edu&g

Re: [Jmol-users] Jmol 14.4.1_2015.12.13 released - IMPORTANT

I have replaced jsmol in FirstGlance in Jmol with the 12/13 version. Indeed the Chrome disaster seems fixed. And in a quick check, FirstGlance appeared to work correctly. Hurray for Bob! I am constantly in awe! (And yes Yay for Mighty Mouse to the rescue!) Mouse rotation in Chrome is still

Re: [Jmol-users] jmolScriptWait vs zoomTo

OK, no problem. Thanks, Bob! -Eric On 12/13/15 8:42 AM, Robert Hanson wrote: Probably a bug that the rest of the script is not executed, but there's no way to wait for a zoomto. Don't do that. On Sat, Dec 12, 2015 at 6:33 PM, Eric Martz <ema...@microbio.umass.edu <mail

[Jmol-users] jmolScriptWait vs zoomTo

Consider the following commands: zoomto *1.3; select protein; color yellow; In javascript, when these commands are in the string "spt", jmolScript(spt) produces a smooth zoom followed by protein turning yellow. However, jmolScriptWait(spt) produces a zoom in one large step (snap zoom) and the

[Jmol-users] Fwd: Chrome: rotation unusable in JSmol

In April 2014, Chrome gave the best performance of JSmol: smoothest rotation and few if any long (~ one minute) pauses during loading of some modest PDB files (pauses seen in Firefox). I configured FirstGlance in Jmol, when using JSmol, to recommend Chrome over Firefox. Safari was good.

[Jmol-users] Bug or feature? (anomalous _P)

Dear Bob, While preparing a morph from 5cl3 to 5cle, I re-ordered the hetero atoms in 5cle so as to be in the same order as the homologous atoms in 5cl3. This separated [3DR]6:B.P from the other 3DR atoms. The result is that this phosphorus, while it remains hetero, is deemed by Jmol to be

Re: [Jmol-users] Zoom calculation

Initial zoom depends, if your Jmol is rectangular, on set zoomlarge and set zoomheight. Just in case you didn't remember those. With zoomlarge true I often set zoom to 110% to pretty much fill Jmol to the edges. -Eric On 12/3/15 7:05 AM, si...@publcif.co.uk wrote: > Dear all > > If I do "rotate

[Jmol-users] DOCUMENTATION dotdensity

Dear Bob, The docs on 'dotdensity' seems obsolete. It appears to me that the default dotdensity is 3, not 0. Also a value of 4 is accepted. Negative values don't seem to work as the docs would suggest. Please update this section. Thanks! Eric

[Jmol-users] DOCUMENTATION cartoon/hermitelevel

Dear Bob, Under 'cartoon', under 'See also', please add set (structure) Although hermite level is mentioned in the introductory paragraph, I don't necessarily look there and am more likely to look under 'see also' when I think there is a relevant setting. Thanks, Eric

Re: [Jmol-users] Capture inter-frame delay

Thanks for banging me over the head, Bob -- I needed it! Indeed I never grasped that animationFPS determines the delay between frames in a multi-GIF from the capture command. I kept mis-reading it as spinFPS. So I've been frustrated for more than a year due to my own denseness. Now I can

Re: [Jmol-users] Capture inter-frame delay

Yes, I can adjust the frame rate with spinfps. But the GIF file that is written unconditionally has a constant 0.1 sec delay between frames. Here are some results: # rotating 360 degrees in 2 sec gives only 60 frames # with default spinfps 30 (frames per second). # 4 sec gives 120 frames with

[Jmol-users] Capture inter-frame delay

Dear Bob, I continue to be frustrated by the lack of control over the otherwise FABULOUS capture command. I first made this request on December 9, 2014. The multi-GIF saved by the capture command plays back with a constant 0.1 second delay between frames. One cannot get a smooth, rapid

[Jmol-users] Writing from browsers

I have tested "write pngj" and "capture" to write files to the local disk from an online HTML page. I also tested the ability to drop a pngj into Jmol in a browser. I tested these 5 browsers (all current versions): Chrome, Edge*, Firefox, Internet Explorer 11* (IE11), Safari#. * Windows

Re: [Jmol-users] loading gzipped files in JSmol - Safari

To anyone testing for Angel, CAUTION: In the email below, the first link is labeled _ATPsintasa_mol.htm_ but the URL it goes to is _ATPsintasa_mol-2.htm!!_ The second link to

Re: [Jmol-users] loading gzipped files in JSmol - Safari

Test results on OS X Yosemite with all browsers up to date. For me, since Yosemite, Safari seems broken. I never use it anymore. After you start Safari, there is a long pause, about 20 sec, before it will load any website. Often you get a "beachball". Sometimes it never loads. You may have to

[Jmol-users] Jmol_S applet crash

Dear Bob, The following crashes the Jmol_S Java applet, version 2015.11.07, in FirstGlance in Jmol. It also crashes Jmol_S applet version 2015.10.17 at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED It does not crash JSmol. I did not succeed in reproducing this in the

Re: [Jmol-users] Help to put Jmol on server for multi-GIF

u can save to the local disk. Hooray! I hope this is intentional, not a bug. Bob, please confirm that this will remain available -- before I spend a lot of time developing a user interface in FirstGlance to save an animation for Powerpoint. -Eric On 11/16/15 2:33 PM, Rolf Huehne wrote: On 11/16/2015 08:2

[Jmol-users] Help to put Jmol on server for multi-GIF

nload. 1. Is this the best solution? 2. If so, will someone please guide me in how to do this? Thanks very much, Eric Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- Martz.MolviZ.Org <http://Martz.MolviZ.Org> * Top Five 3D MolVis Tools: Top5.MolviZ.Org <htt

Re: [Jmol-users] Help to put Jmol on server for multi-GIF

DOUBLE HOORAY!!! So I will begin coding a user interface to use capture from the applet in a browser. Thanks Bob, -Eric On 11/16/15 6:34 PM, Robert Hanson wrote: public boolean allowCapture() { return !isApplet || isSignedApplet; } Eric, I must have misunderstood you -- I meant no

[Jmol-users] PNGJ loading bug in OS X

This bug may not be worth fixing since it is specific to OS X, and may be a bug in Java. Using either the Java applet, or the Jmol application, the command write "test.pngj" saves a file that contains the atomic coordinates and the state of Jmol. In *Windows*, dragging this PNGJ file into

[Jmol-users] FirstGlance updated

patibility and performance has been updated, and the Edge browser in Windows 10 has been included. See http://bioinformatics.org/firstglance/fgij/notes.htm#browsers As always, thanks to Bob Hanson for his responsiveness in diagnosing and fixing a number of bugs. -Eric Eric Martz, Professor Emer

[Jmol-users] Installing & Enabling Java (Updated)

These instructions for installing and enabling Java http://proteopedia.org/w/Installing_and_enabling_Java have been updated to include Microsoft Edge, a browser first released as part of Windows 10. Edge does not support Java. However Internet Explorer 11 is also included in Windows 10, and

[Jmol-users] JSmol in Edge, Chrome, etc.

My tests of JSmol (in FirstGlance) in the Windows 10 Edge browser indicate that while Edge runs HTML5/Javascript much faster than Internet Explorer, it is still markedly slower than Chrome or Firefox. Internet Explorer remains unusably slow with JSmol/HTML5. Edge is usable but sluggish,

[Jmol-users] Oct 17 Jmol works in FirstGlance

Hey Bob, thanks so much for your prompt efforts fixing bugs. The Oct 17 release (which is still named 14.4.0_2015.10.14, but shows the date below the version number as Oct 17) appears to work correctly with all FirstGlance operations. And Halleleujah! Now the JSmol menu can be popped up in

[Jmol-users] DNA sidechain bug

Dear Bob, With Jmol October 14: Many DNA oxygens that are not sidechain atoms are selected with "select dna and sidechain", notably oxygens on phosphorus and in deoxyribose. load =1d66 restrict none select dna and sidechain wireframe 0.3 spacefill 0.3 color cpk You will see the sidechains of

Re: [Jmol-users] All deployed Jmol Java applets are disabled

Are you sure its *irrevocable*, Bob? That's quite unfortunate. As Angel says, it will take me some time to verify that current Jmol works in FirstGlance. Typically, I find one or more bugs/issues and have to wait till they're fixed (in my code or in Jmol) before I release a new version. And

[Jmol-users] Unsigned Jmol Java applets still work

Curiously, very old websites that still use unsigned Jmol java applets still work, despite the certificate for newer signed Jmol being revoked. For example, the tutorials on Hemoglobin, Antibody, and MHC at http://molviz.org. These still work in Firefox on OS 10.10.5 Yosemite. An alert

[Jmol-users] 14.4.0 problem with HTML5

Dear Bob, While developing FirstGlance, I test by running from local files in Firefox (on OS X; currently Firefox 41.0.2). All tests below were done using *HTML5* (no Java). My current in-progress version of FirstGlance loads and displays 1d66 using JSmol from *Sept 20*. Function appears

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