[Jmol-users] messaging arbitrary signal strings

for messaging an arbitrary string, I am using this scheme: set debugscript on define arbitrary_signal_1 none set debugscript off Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis

[Jmol-users] messaging arbitrary signal strings

for messaging an arbitrary string, I am using this scheme: set debugscript on define arbitrary_signal_1 none set debugscript off Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis

[Jmol-users] Release notes for Jmol 10.3 or 11?

I see that Jmol prerelease 10.3.1 is available for download. Can someone give me the URL for the notes about what the changes are in 10.3 and 10.3.1? Ditto for Jmol 11 (and where is the download?)? Thanks, -Eric - Using

Re: [Jmol-users] messaging arbitrary signal strings

At 8/11/06, you wrote: Eric, the command is echo. Just make sure you have set echo off so that the user does not get the message as well. I see that this does not require 'set debugscript on', which is good. However, 'set echo off' erases the current message for the user (in Jmol). This is

Re: [Jmol-users] Jmol's cartoon rendering needs improvements

At 8/12/06, you wrote: Eric, as I think about this, I realize that you are referring to the rockets rather than the cartoons. Is there something about the *cartoons* that you don't like? -- They are the objects that are meant to replace the Chime cartoons. Jmol cartoons behave as you describe you

[Jmol-users] Bugs that HIDE DOTS inappropriately

. It would be great to have them fixed! Thanks, -Eric Eric Martz, Professor Emeritus, Dept Microbiology University of Massachusetts, Amherst MA US http://www.umass.edu/molvis/martz - Using Tomcat but need to do more? Need

Re: [Jmol-users] variable dots density?

://lists.sourceforge.net/lists/listinfo/jmol-users /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http

[Jmol-users] Proposing set labelsFront group

. Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org Protein

[Jmol-users] Recent MolVis articles in BAMBEd

and a microphone encoded the data! -Eric Eric Martz, Professor Emeritus, Dept Microbiology University of Massachusetts, Amherst MA US http://www.umass.edu/molvis/martz - Using Tomcat but need to do more? Need

[Jmol-users] Slab picking: serious deficiency

/* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org Protein Explorer - 3D

[Jmol-users] Lots of bugs in Jmol: fix some before v11?

it. I hope some of these bugs can be fixed before v11 comes out. Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources http://MolviZ.org See 3D

[Jmol-users] NO LONGER stuck on show pdbheader

OK, I solved my show pdbheader problem easily enough. The problem was not in the show pdbheader or messageCallback() mechanisms, but rather in the workaround I used to send arbitrary messages (to signal the beginning and end of the pdbheader message). I'm not sure why that workaround no longer

Re: [Jmol-users] Jmol - deuterium and tritium - colors

you please post your views to jmol-developers (or users), so that this is set before official 11.0 is out? /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources

[Jmol-users] Want Z rotation separate from Zoom

, -Eric Eric Martz, Professor Emeritus, Dept Microbiology University of Massachusetts, Amherst MA US http://www.umass.edu/molvis/martz - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel

Re: [Jmol-users] Lots of bugs in Jmol: fix some before v11?

I have inserted my responses in red. Hope this works. I did my tests with 10.9.64 and 10.9.67 applets. -Eric On 9/23/06, Bob Hanson wrote: Synopsis 1) Calcium as protein is fixed in 10.9.61. I agree that it is fixed! 2) The problem with situations where there are two groups in the same

[Jmol-users] Wiki to compare molecular viewer features

/* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org Protein Explorer - 3D

[Jmol-users] CORRECTED Molecular viewers in the literature

At 9/30/06, Egon Willighagen wrote: On Saturday 30 September 2006 03:40, Eric Martz wrote: Numbers of hits searching full text of scientific journals at highwire.stanford.edu: 2,364 Jmol Pardon?? Theses are Jmol word counts, correct? Any idea on the number of article this corresponds

Re: [Jmol-users] Chime Sculpt mode?

/listinfo/jmol-users /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org Protein

Re: [Jmol-users] issue with message callbacks and internationalization

/* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org Protein Explorer - 3D Visualization: http

Re: [Jmol-users] issue with message callbacks and internationalization

At 10/13/2006, Bob H wrote: and message callback is not the issue, since there are other modes of getting the same information. It is my understanding that no other method works on all the platforms we wish to support. That is why I have continued to use messagecallback. -Eric

Re: [Jmol-users] Dynamic popup menu: grayed-out groups

At 10/13/2006, Bob wrote: shall we count them, too? ALA (3) ARG (2) ... etc? That would be even better. -Eric - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with

Re: [Jmol-users] issue with message callbacks and internationalization

At 10/13/2006, Bob H wrote: I think I have a simple solution. Your plan sounds good to me, Bob. Thanks for thinking it through! -Eric - Using Tomcat but need to do more? Need to support web services, security? Get stuff

Re: [Jmol-users] Dynamic popup menu: grayed-out groups

I don't think its important. If there is a significant time penalty, let's skip the count. At 10/13/2006, you wrote: how much of a hit are you willing to take on time to catalog all these? Bob Eric Martz wrote: At 10/13/2006, Bob wrote: shall we count them, too? ALA (3) ARG (2

[Jmol-users] Molecular 3D Visualization Servers

, and rotating multi-GIFs -- ready to paste into Powerpoint! /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing

[Jmol-users] Jmol applet for beginners?

What resources are appropriate for a high school teacher who wants his students to develop website projects using Jmol? Where are the best Jmol resources for beginners who want to make their own web pages with the Jmol applet? Thanks, -Eric Eric Martz, Professor Emeritus, Dept

Re: [Jmol-users] show state -- Jmol serialization

look forward to its further development!! -Eric Eric Martz, Professor Emeritus, Dept Microbiology University of Massachusetts, Amherst MA US http://www.umass.edu/molvis/martz - Using Tomcat but need to do more? Need

Re: [Jmol-users] history records failed commands

@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources http://MolviZ.org See 3D

[Jmol-users] Show state OUTSTANDING! ( minor bugs)

Dear Bob, Frieda and I tried show state, then pasting the resulting script back into the console (in a different Jmol applet session after a zap). WOW. CONGRATULATIONS BOB! WE WERE BLOWN AWAY WITH HOW WELL THIS IS WORKING!!! In two very different, complicated views, we were able to regenerate

[Jmol-users] Absolute Zoom (Viewport Angstroms)?

Angstroms refer to the horizontal or vertical size, or to the average of those, provided the mechanism is clearly stated. Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz

[Jmol-users] Requesting absolute-scale zoom pretty please

set scale3D is useful but does not meet my needs for an absolute-scale zoom. I can live with set perspectivedepth off if that is required for absolute scaling. I need a way to zoom SMOOTHLY from any arbitrary starting point (such as reset) to (for example) where 50 Angstroms will fill 500

[Jmol-users] zoomto bug

zoomto should do, but maybe this bug is easy to fix? Thanks, Bob --Eric Eric Martz, Professor Emeritus, Dept Microbiology University of Massachusetts, Amherst MA US http://www.umass.edu/molvis/martz - Take Surveys. Earn

[Jmol-users] Bug in font label ...

In Jmol 11.1.0, and also 10.9.105, a certain sequence of commands disables the font label command. That is, the font label command has no effect. The following test results are for 11.1.0. I get this condition when set labelfront and select none (in either order) are followed by font label

[Jmol-users] Multiple colors within an echo line

a single echo string? We and likely others would find this useful in many contexts. Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources http

Re: [Jmol-users] Jmol bug fixes

At 12/15/2006, you wrote: I do NOT plan to introduce this as a bug fix to 11.0 even though I think it is a bug. This is because I think 11.0 should not have any visible changes relative to 10.2. Sounds like a fine plan to me! -Eric And thanks for fixing all the issues I reported, Bob

[Jmol-users] Need levels for debugscript reports

I would like to second Frieda's plea (Sept. 22, subject Re: [Jmol-users] Prerelease 10.9.62) for restoring set debugscript on to usefulness for our purposes. Through 10.2, it was extremely useful to us. Since then, it generates far too much information, making it nearly impossible to find a

Re: [Jmol-users] message command

___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D

Re: [Jmol-users] How to merge two pdb file?

-users /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org Protein Explorer

Re: [Jmol-users] How to merge two pdb file?

discussion. -Eric At 2/11/2007, Qiang Zhong wrote: Dear Eric Martz: I will very happy to tell you what I want to do,and eager to receive your letter.there are two molecular protein_A and protein_B. Protein_A is a enzyme, it have a target peptide, Protein_B is a regulatory protein

Re: [Jmol-users] [Molvis-list] BioMolecular Explorer 3D, version 2 - in Jmol

there, go to http://molvisindex.org, click on K-12 resources, and then on the Submit or Revise links. You just fill out a short form with the link. We need more good K-12 molecular visualization resources there! -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz

Re: [Jmol-users] [Molvis-list] Contact and request for support

miss http://balloonmolecules.com !! Finally, for junior-high students, there is a cool, easy, on-line workalike to DNA fingerprinting here: http://www.moleculesinmotion.com/alphabet_traits/ Sincerely, /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept

[Jmol-users] Intel-based Macs and Shockwave/Java/Rosetta

I just became aware of a Jmol issue that occurs only on Intel Macs. Sorry if this is already a known topic on jmol-users. If you want to use Shockwave in Safari or Firefox, you have to enable Rosetta (PPC) mode, because apparently there is no Shockwave for Intel Macs yet. Rosetta mode disables

[Jmol-users] Jmol anim(ations) too slow

uncompressed. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org Protein

[Jmol-users] One Laptop Per Child project vs. java/Jmol

The One Laptop Per Child project is really fascinating and amazing. Imagine a linux-based network-capable $100 laptop that can work on human (pedal or crank) power, designed for learning in technology-remote areas of the world. They aren't quite in production yet, but Nigeria has ordered a

[Jmol-users] Fwd: Use statistics on macro-molecular visualization programs

Date: Sun, 27 May 2007 12:52:22 +0900 To: Lizanne Huysamen [EMAIL PROTECTED] From: Eric Martz [EMAIL PROTECTED] Subject: Use statistics on macro-molecular visualization programs Cc: [EMAIL PROTECTED], [EMAIL PROTECTED], [EMAIL PROTECTED] At 5/25/2007, Liz Huysamen wrote: Dear Mr Martz I'm

[Jmol-users] Animation: pause/resume, and unwanted frame skipping

, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org Protein Explorer

Re: [Jmol-users] Animation: pause/resume, and unwanted frame skipping

At 6/7/2007, Angel Herraez wrote: I have two buttons that do anim on and anim off. The problem is that although anim off freezes the animation at its current position (or close to it), anim on starts over from frame 1. One wants to stop the animation at a specific point, then resume it

Re: [Jmol-users] Animation: pause/resume, and unwanted frame skipping

At 6/10/2007, you wrote: Eric, it is very important to us that you download the latest version (11.1.47, I think) and try it. Please let me know as soon as possible whether animation no longer skips frames for you and otherwise works as expected. I'd like to make sure we have this right before

[Jmol-users] Bugs in 11.2.0-11.3.0: hover, zoomto (center)

(WAY off the intended center) zoomto (59-75) script 23 started zoomTo ( ( 59 -75 ) ) Script completed -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education

[Jmol-users] Command alias support in Jmol?

know (on list or off list as you prefer). -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing

[Jmol-users] Bad experience editing wiki

I was just trying to update my entry EricMartz at the Jmol wiki (http://wiki.jmol.org:81/index.php/Main_Page). Apparently due to a few minutes of inactivity, I was auto-logged out, which almost caused me to lose significant editing work. I recommend that the auto-logout time be increased to 60

[Jmol-users] Remediated PDB format v3 vs. Jmol?

Dear Bob, Herb Bernstein's recent message to molvis-list and pdb-l about RasMol being revised to support PDB format version 3 alerted me to a potential problem that I had not been aware of. As part of the PDB's remediation project ( http://remediation.wwpdb.org/ ), they made changes to the

[Jmol-users] Jmol tutorials now at MolviZ.Org

to learn how to use PyMol. Chime-based resources are now described as being phased out, but will remain available as long as they are used. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis

[Jmol-users] New menu item Identity?

At 7/24/07, Bob Hanson wrote: translations needed for the new Identity menu item. The only Identity item I find on the menu of 11.3.6 is under Set Picking. Is that the new item to which you refer? - This SF.net email is

Re: [Jmol-users] Remediated PDB format v3 vs. Jmol?

Dear Bob, I have now done some tests on nucleic acids for the old vs. new PDB formats. The old format, version 2.3, has been in effect since 1998. The new remediated version goes into effect August 1, 2007. Differences are summarized in http://www.wwpdb.org/documentation/format3.1-20070719.pdf

[Jmol-users] Mouse synchronization between 2 or more jmol applets

/chimeembed.jsp#sendmouse The corresponding section on target is not complete/correct. Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources http

[Jmol-users] Top 5 MolVis Resources (eliminating Chime)

at http://MolviZ.Org/top5.htm Or simply go to http://MolviZ.Org and click on MolviZ Top 5. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources http

[Jmol-users] Script buttons for multiple Jmols

discussed). I do plan to see if that can be implemented satisfactorily. Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources http://MolviZ.org See 3D

[Jmol-users] Premature/unwanted ball stick in 11.3.11

It appears to me that a premature/unwanted default ball and stick display of the loaded molecule (before the scripted view) began occurring in Jmol 11.3.9-11. This did not happen in Jmol 11.3.7 or earlier. I observe this in FirstGlance in Jmol. Here, the param script=... in the applet ... tag

Re: [Jmol-users] Jmol 11.3.15 -- custom menus

). Perhaps these could be brief explanations, with links that open a new browser window and go to the full explanation? Just a thought. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis

[Jmol-users] FirstGlance in Jmol 1.01: DNA chain selection fixed

, documentation, and testing are not yet complete. It is used for the ConSurf, Pepitope, and Selecton servers, and the OCA PDB service. I have also updated the list of adoptions and adaptations of FirstGlance in Jmol. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz

[Jmol-users] Simplest spin toggle command?

/* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Top Five 3D MolVis Technologies http://Top5.MolviZ.Org Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http

Re: [Jmol-users] Simplest spin toggle command?

Thanks for promptly telling me the solution, Bob, as always. It works!! -Eric - SF.Net email is sponsored by: The Future of Linux Business White Paper from Novell. From the desktop to the data center, Linux is going

[Jmol-users] Multiple Jmols in Tutorial Template

that the code common to all tutorials is separated from the code specific to a given tutorial. Multiple tutorials can exist in side-by-side directories, and all share one jmolApplet.jar + Jmol.js. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus

[Jmol-users] Sync-ing different molecules

/* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Top Five 3D MolVis Technologies http://Top5.MolviZ.Org Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing

Re: [Jmol-users] Sync-ing different molecules

in the code that generates this command and sends it to the other applet, we could certainly modify that to suit. What subset would you like? Maybe just the rotation part? That would be easy enough. Something like set syncRotationOnly perhaps. Eric Martz wrote: I am using sync in my Jmol

Re: [Jmol-users] Sync-ing different molecules

At 12/11/07, you wrote: It will have to be considerably more than that, and for this sort of very specific set, I have to be convinced that what we would get would be a natural expectation. In Chime, it works very intuitively. For example, in slide 5 here http://tinyurl.com/2fy7ol rotate/zoom the

Re: [Jmol-users] Loading several models at once

-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Top Five 3D MolVis Technologies

Re: [Jmol-users] Sync-ing different molecules

At 12/13/07, you wrote: Eric, could you please try the latest at http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11_3.zip ? I'm hoping this does the job. Dear Bob, Using Jmol applet 11.3.57_dev December 12, 15:56: Watching two unaligned different molecules rotate in synch, using the

Re: [Jmol-users] Sync-ing different molecules

At 12/13/07, you wrote: But I think you should be able to LOCK the two models the way you are suggesting so that either one when you move it drags the other around. Sort of a mutual sync. I'll have to think about why that is not happening when you use sync * ON. Again, my desire is that users

Re: [Jmol-users] memory allocation

Here are the results of my testing of my Jmol Tutorial-Authoring Template, which supports 1, 2, 3 or 4 Jmols per view button. I certainly hope not to have to ask users of a Tutorial to open their java console and orce garbage collection. So I didn't do that. Nor do I want them to have to

[Jmol-users] 11.3.58 seems DOA

applet inappropriately sets syncMouse off for itself and starts sending moveto commands back to the first applet. That will be fixed in 11.3.58. Bob Eric Martz wrote: At 12/13/07, you wrote: But I think you should be able to LOCK the two models the way you are suggesting so that either one

Re: [Jmol-users] Sync-ing different molecules

Dear Bob, Sync is now FANTASTIC (applet 11.3.59)! The functionality is as smooth as Chime's and, like Chime, you can now sync different (not aligned) molecules beautifully. And you've added functionality that Chime didn't have (set syncScript). And importantly, Chime's synch was never

Re: [Jmol-users] Fwd: cannot view molecules

/* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Top Five 3D MolVis Technologies http://Top5.MolviZ.Org Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing

[Jmol-users] Can jmol initiate zoom change messages? (re: zoom slider)

I installed the very nice slab slider available from http://wiki.jmol.org:81/index.php/Recycling_Corner#Slider_control_for_Slabbing in my Jmol Tutorial-Authoring Template (JTAT). I have now adapted it to control either zoom or slab. I would like the zoom slider to auto-slide to match the current

[Jmol-users] Free copy of book How to Use Jmol ...

I have an extra copy of Angel Herraez's new book How to use Jmol to study and present molecular structures, Vol. 1: Learning to use Jmol (basic and intermediate levels). If you would like it, just email your snail mail address to me (off-list). -Eric Eric Martz, Professor Emeritus, Dept

[Jmol-users] Message contents of .spt file without execution?

Sometimes I wish that, from javascript in the browser, I could ask the Jmol applet to let me (javascript) peek into the contents of a Jmol command script (.spt) file, preferably before I execute it. Is there some way to do this? If not, do others think this would be useful? I'm envisioning

[Jmol-users] picking center -zoom, +pickCallback?

I would like to click on an atom, and have the molecule move slowly to make that atom the new center. This is exactly what set picking center now does. However, set picking center zooms 2x if you click the same atom again, and zooms 1/2x if you click and miss the atom. I definitely do not

Re: [Jmol-users] Message contents of .spt file without execution?

to the current page (not necessarily the directory containing the applet) and must be enclosed in quotation marks. Paul Le 12 janv. 08 à 04:55, Eric Martz a écrit : Sometimes I wish that, from javascript in the browser, I could ask the Jmol applet to let me (javascript) peek into the contents of a Jmol

Re: [Jmol-users] picking center -zoom, +pickCallback?

the zoomto command. Furthermore, I can then turn centering mode (in my javascript) off after one click. This solves everything. Thanks again, -Eric At 1/13/08, you wrote: Eric, your question is complex, but for now I have an answer for a part of it: On 12 Jan 2008 at 17:57, Eric Martz wrote

[Jmol-users] bugs in set echo and its documentation

I love the fact that you can name an echo, display it, then operate on a second named echo without affecting the first. This is a super feature! However: The following invalid argument results appear to me to be bugs in set echo, in Jmol applet 11.4.RC1, as it is documented: set echo off #

[Jmol-users] Serious Memory Issue in Jmol/JTAT

RE: Jmol Tutorial-Authoring Template (JTAT), nearing release (I hope). Near final demo at http://bioinformatics.org/jmol-tutorials There is a major unresolved problem which calls into question the usability of tutorials using Jmol, and JTAT in particular: running out of java memory. In

Re: [Jmol-users] for loop question

At 1/21/08, you wrote: Can a for loop in Jmol take two variables, as follows? for ( var i = -9, j = 2; i -4.0; i = i + 0.2, j = j + 1 ) So far I have not had success, j seems to have no value where as i is working fine. What would be wrong with this: var j = 2; for (var i = -9; i -4.0; i

Re: [Jmol-users] Serious Memory Issue in Jmol/JTAT

Dear Bob and Angel and others, I will certainly appreciate your help regarding the memory problems that I'm having with JTAT! 1. YES I AM using Jmol.js in JTAT. (I did not use it in FirstGlance in Jmol because it seems to me inadequately documented, and because I felt I needed to understand

[Jmol-users] Need show _memory to work, with 3 values

I am spending hours/days doing tests on the total (used) memory reported in the Jmol applet menu. For every step, I have to manually open the Jmol menu and hand record the total memory and free memory values. Although there is supposed to be a read-only _memory, show _memory returns not set

[Jmol-users] Zeroing delays, instant moveTo's for fast retesting

, and all your delays and moveTo's work as intended. If anyone else would find this useful, please chime in. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Top Five 3D MolVis

[Jmol-users] Zeroing delays, instant moveTo's for fast retesting

setting, and all your delays and moveTo's work as intended. If anyone else would find this useful, please chime in. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Top Five 3D MolVis

[Jmol-users] Fwd: MolySym looking for molecular visualization software engineer

Date: Thu, 24 Jan 2008 22:55:55 -0500 From: Woody Sherman [EMAIL PROTECTED] To: [EMAIL PROTECTED] Subject: MolySym looking for molecular visualization software engineer Hi Eric, Hope all is going well. Since the last time we met in your office we ended up getting an SBIR Fast-Track grant from

Re: [Jmol-users] un/loading the jmol Applet

/listinfo/jmol-users Eric Martz, Professor Emeritus, Dept Microbiology University of Massachusetts, Amherst MA US http://www.umass.edu/molvis/martz - This SF.net email is sponsored by: Microsoft Defy all challenges

[Jmol-users] Sync centering bug

At 1/30/08, you wrote: 1. In addition to the controls you already have below the Jmols, a checkbox to synchronize mouse-directed rotations and zooms would be cool. See sync in the manual. I use sync * on and sync * off (* = all Jmols) together with set syncScript false; set syncMouse

[Jmol-users] Reporting applet id to console

I recall there is a command (show something?) that reports information about the applet into the console, including the applet's id (e.g. jmolApplet0, jmolApplet1, etc.) but I cannot recall or find how to do this. Can someone please remind me? Perhaps the applet id should be listed on the menu

Re: [Jmol-users] Reporting applet id to console

Si si, Angel. ¡Muchas gracias! At 2/4/08, you wrote: Hi Eric may that be getProperty appletInfo ? http://chemapps.stolaf.edu/jmol/docs/?ver=11.4#getProperty - This SF.net email is sponsored by: Microsoft Defy all

Re: [Jmol-users] browser memory and threading issues

At 2/1/08, Bob wrote: The page http://www.stolaf.edu/people/hansonr/jmol/test/new/simple4.htm allows testing of two browser issues: 1) Reloading Jmol into a DIV using div.innerHTML = ... My observations: I see no problems on Firefox/Windows, MSIE/Windows, Firefox/Mac, Safari/Mac. All create new

[Jmol-users] Jmol resizing problem in Safari 3/OS 10.5

Dear Angel, As you know, I am using your resizable.js in my Jmol Tutorial-Authoring Template. http://bioinformatics.org/jmol-tutorials In IE and FF (Windows), both Jmol and a text division resize/rewrap automatically. I just noticed that when you resize the Safari window, neither the text

Re: [Jmol-users] browser memory and threading issues

Dear Bob, Thanks for your suggestions. I'll give them a try ASAP. Meanwhile, I discovered another symptom. In the simple test pages, zap zap (two zaps one right after the other) always reduces total memory to a low value (9-12 Mb). However, in the JTAT Demo, zap zap never reduces total

Re: [Jmol-users] browser memory and threading issues

At 2/6/08, Rolf wrote: I tried some of your demo tutorial pages (e.g.: http://www.bioinformatics.org/jmol-tutorials/jtat/jtatdemo/ch_comp/chapter.htm) with Firefox 2.0.0.10 on Linux and noticed the following: 1) Synchronization didn't work at all. 2) The zoom slider is not refreshed if the zoom

Re: [Jmol-users] browser memory and threading issues

At 2/6/08, you wrote: Eric, I found the memory leak. Dear Bob, Yes you did! Hooray! I haven't any idea how you do these amazing things with Jmol, but I am tremendously impressed and grateful! I can now go through the entire JTAT Demo Tutorial (skipping Chapter 2, view 2) with total memory

[Jmol-users] Echo size bug with antialiasing

JTAT has a script that gradually reduces an echo font size from 24 to 16, like this font echo 24 sans bold delay 0.1 font echo 23 sans bold delay 0.1 font echo 22 sans bold delay 0.1 font echo 21 sans bold delay 0.1 font echo 20 sans bold delay 0.1 font echo 19 sans bold delay 0.1 font echo 18

[Jmol-users] Jmol applet javascript on linux

) when the problem is occurring? If total is about equal to max then you may be running out of java memory. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Top Five 3D MolVis

[Jmol-users] Menu lacking temperature color scheme

It appears to me that Jmol 11.5.5_dev is lacking temperature as a By Scheme coloring on the Color menus. The command color atoms temperature works. This highly informative color scheme should be included on the menus, in my opinion. For a brief introduction to crystallographic temperature or

Re: [Jmol-users] [Fwd: paper What's new for Jmol successfully submitted]

/polyview3d.html ) /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Top Five 3D MolVis Technologies http://Top5.MolviZ.Org Biochem 3D Education Resources http://MolviZ.org See 3D Molecules

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