[Jmol-users] MacOS X browsers and Jmol.app

Hey folks, OK, I downloaded XCode and created Jmol.app per Tim & Henry's instructions, and it worked! So now I have a Jmol application that MacOS X recognizes as an application. Now the bad news. Netscape 7.1: I could create a MIME type and extension and give the browser instructions as to

[Jmol-users] oops

Mistyped the web address! I have followed the instructions about making jmol into a Mac application. I have placed the result at the following web address for anyone interested in downloading. No guarantees :) http://www.saintmarys.edu/~pbays/jmol/jmol.htm Now when someone teaches Opera or

[Jmol-users] jmol as an application

I have followed the instructions about making jmol into a Mac application. I have placed the result at the following web address for anyone interested in downloading. No guarantees :) http://www,saintmarys.edu/~pbays/jmol/jmol.htm Now when someone teaches Opera or anything else to open it, t

Re: [Jmol-users] Measurements in JmolApplet

At 3/18/04, Miguel Howard wrote: >>>like in RasMol, if I said: >>> set picking distance >>>Atom #1: [ARG]97:E.NH2 (1062) >>>Atom #2: [ARG]173:E.NH2 (1722) >>>Distance [ARG]97:E.NH2 - [ARG]173:E.NH2 = 19.211 >> >>Are you saying that you get all this text sent to you as a single >> string? >> > yes,

[Jmol-users] How to make the Jmol.jar application launchable on MacOSX

Bob wrote: > Henry, can you give detailed directions for someone who doesn't know > anything about Java, beginning with where I get the developer kit and > how I install it? Here are Henry's instructions ... along with a Step 0 and Step 5 from Tim Driscoll. Miguel step 0. a. if you installed

[Jmol-users] Re: browsers & Jmol

Title: Re: browsers & Jmol Just saw an announcement about the new version of Opera.   I have a beta version.   It appears to have the ability to specify helper aps, unlike anything else, and is supposed to have LiveConnect when complete ... soon they say.  I have not had time to try the mime desi

Re: [Jmol-users] Browser enhancement technologies tutorial

It is a shame to relegate this truly superb tutorial (Thanks, Miguel!!) to the email list. Because of the high volume on jmol-users, I don't think it works well for looking up things (but maybe I don't know how?). I think the jmol.sourceforge.net site needs a place where people can submit and a

Re: [Jmol-users] MDL refusal to open Chime source code

At 3/17/04, Robert B. Grossman wrote: By the way, MDL confirms that they won't release the source code for Chime, even on a confidential basis. I don't understand why not; it's no good to them anymore. But it's their property to do with what they will, I suppose. One reason MDL has given in th

[Jmol-users] browsers

Just saw an announcement about the new version of Opera. I have a beta version. It appears to have the ability to specify helper aps, unlike anything else, and is supposed to have LiveConnect when complete ... soon they say. I have not had time to try the mime designation yet. Will this he

[Jmol-users] RE: set picking and shift left zoom

Hello again Miguel Howard wrote: >>And I want to put functionality into the applet so that people can use it >>without writing scripts. Hence the measurement functionality. Eric Martz wrote: >I agree that this is very good for power users (perhaps 1% of the potential >Jmol users). >However, the

[Jmol-users] Re: select [5MC]2498B -> FIXED

> with 1c2w I got the following error: > 3 letter residue specification expected : select [5MC]2498B; > and there are others, e.g. [5MU]1939B, [7MG]2069B, [1MA]2030B Fixed and checked in. The problem was that caused by the fact that the group/residue names start with digits. Do you happen to kno

Re: [Jmol-users] Re: 3 letter residue specification expected : select [5MC]2498B;

Miguel Howard schrieb: Hi Miguel, with 1c2w I got the following error: 3 letter residue specification expected : select [5MC]2498B; and there are others, e.g. [5MU]1939B, [7MG]2069B, [1MA]2030B Which PDB file? pdb1c2w.ent http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=1c2w Did this work b

[Jmol-users] Re: 3 letter residue specification expected : select [5MC]2498B;

Jan & Miguel wrote: >> with 1c2w I got the following error: >> 3 letter residue specification expected : select [5MC]2498B; >> and there are others, e.g. [5MU]1939B, [7MG]2069B, [1MA]2030B > > Which PDB file? Sorry ... I see ... 1c2w Miguel --

Re: [Jmol-users] Measurements in JmolApplet

>>>like in RasMol, if I said: >>> set picking distance >>>Atom #1: [ARG]97:E.NH2 (1062) >>>Atom #2: [ARG]173:E.NH2 (1722) >>>Distance [ARG]97:E.NH2 - [ARG]173:E.NH2 = 19.211 >> >>Are you saying that you get all this text sent to you as a single >> string? >> > yes, in RasMol But does it happen in

Re: [Jmol-users] Jmol as an application on OS X

>Rzepa, Henry sent [10.43a gmt 2004 March 18 Thursday] : > >>Found a mechanism to wrap the Jmol.jar into an application on OS >>X (thus converting it to jmol.app ) which CAN be treated as a >>proper application. Use /Developer/Applications/Java Tools/Jar >>Bundler and indicate the main class

Re: [Jmol-users] Measurements in JmolApplet

Miguel Howard schrieb: Jan wrote: please keep this compatible with single click and PickCallBack Single click should now call the PickCallBack OK, set picking ident is the default. It is the default ... and there currently is nothing else. and give a MessageCallBack whi

[Jmol-users] Re: 3 letter residue specification expected : select [5MC]2498B;

> Hi Miguel, > with 1c2w I got the following error: > 3 letter residue specification expected : select [5MC]2498B; > and there are others, e.g. [5MU]1939B, [7MG]2069B, [1MA]2030B Which PDB file? Did this work before and get broken as a result of my recent changes to support x/y/z ? Miguel

Re: [Jmol-users] Jmol as an application on OS X

Henry wrote: > Found a mechanism to wrap the Jmol.jar into an application on OS X > (thus converting it to jmol.app ) which CAN be treated as a proper > application. Use /Developer/Applications/Java Tools/Jar Bundler > and indicate the main class as org.openscience.jmol.app.Jmol Good. > Wh

Re: [Jmol-users] Jmol as an application on OS X

Rzepa, Henry sent [10.43a gmt 2004 March 18 Thursday] : >Found a mechanism to wrap the Jmol.jar into an application on OS >X (thus converting it to jmol.app ) which CAN be treated as a >proper application. Use /Developer/Applications/Java Tools/Jar >Bundler and indicate the main class as or

[Jmol-users] Jmol as an application on OS X

Found a mechanism to wrap the Jmol.jar into an application on OS X (thus converting it to jmol.app ) which CAN be treated as a proper application. Use /Developer/Applications/Java Tools/Jar Bundler and indicate the main class as org.openscience.jmol.app.Jmol Whilst I doubt its worth distr

Re: [Jmol-users] Re: Jmol-users digest, Vol 1 #252 - 11 msgs

Robert wrote: > But we have lots of talented > computer science graduate students here, all looking for challenging > master's projects. Lots of free labor! I'll ask around. If you can find a graduate student that is self-motiviated and if you can provide a small amount of management from your

Re: Pluglets (was: [Jmol-users] Browser enhancement technologies tutorial)

Egon wrote: > I would like to add a possible option: > > http://www.mozilla.org/projects/blackwood/java-plugins/ > > It's been around for years now, but it is not mainstream (yet)... > > Pluglets: mozilla plugins written in Java. > > I have absolutely no idea what the current status is of this proj

Re: [Jmol-users] Browser enhancement technologies tutorial

>> The web browser will launch MS Word every time it sees a >> document with the mime-type 'application/msword'. < > Can I add only to this section that MIME types were never originally > intended for use within browsers; they were supposed to be used only for > email Very true. > In the early da

Pluglets (was: [Jmol-users] Browser enhancement technologies tutorial)

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On Thursday 18 March 2004 09:24, Rzepa, Henry wrote: > Thanks Miguel for a truly excellent and clear summary! I would like to add a possible option: http://www.mozilla.org/projects/blackwood/java-plugins/ It's been around for years now, but it is no

Re: [Jmol-users] Re: shift-left zoom

Tim wrote: >>Unfortunately, Java has no 'Human Interface Guidelines'. It is >>*supposed* to run on all platforms and be agnostic to the platform that >> it is running on. >> > > what about this? > > :-) Very good! Miguel

Re: [Jmol-users] Browser enhancement technologies tutorial

Thanks Miguel for a truly excellent and clear summary! >Plug-in >--- >To understand a plug-in it is helpful to think back to the helper >application. A helper application is not associated with a specific web >page. Rather, it is associated with a specific file type, a specific >mime-type. Th