Jmol is *not* using Java3D. A primary motivation for this is to enable us to run on a wide variety of platforms.
The current released version, Jmol 7, does not have true 3D capabilities. It uses the painter's algorithm, rendering the shapes back to front. However, it does not deal well with intersecting shapes. The development version has a z-buffer engine implemented in Java. It has true 3D capabilities and properly deals with intersecting objects. It provides a platform for the rendering of iso-surfaces, orbitals, and protein visualization shapes. Additionally, it offers significantly higher performance for larger molecules. This will be released as Jmol 10 within the next few months. Miguel > Hi All, > > I am new to this list. I am interested to know if > JMol is using Java3D ? > > Cheers, > Sione. > > > ----- Original Message ----- > From: <[EMAIL PROTECTED]> > To: <[EMAIL PROTECTED]> > Sent: Thursday, October 02, 2003 3:12 PM > Subject: Jmol-developers digest, Vol 1 #289 - 9 msgs > > >> Send Jmol-developers mailing list submissions to >> [EMAIL PROTECTED] >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://lists.sourceforge.net/lists/listinfo/jmol-developers >> or, via email, send a message with subject or body 'help' to >> [EMAIL PROTECTED] >> >> You can reach the person managing the list at >> [EMAIL PROTECTED] >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Jmol-developers digest..." >> >> >> Today's Topics: >> >> 1. 0-based vs 1-based atom numbering (Miguel) >> 2. Atom numbering in RasMol/Chime -- feature or bug? (Miguel) 3. [ >> jmol-Bugs-815789 ] What to do about label fontsize > (SourceForge.net) >> 4. Re: 0-based vs 1-based atom numbering (Peter Murray-Rust) >> 5. Re: Atom numbering in RasMol/Chime -- >> feature or bug? (Peter Murray-Rust) >> 6. Re: 0-based vs 1-based atom numbering (Miguel) >> 7. Re: 0-based vs 1-based atom numbering (Miguel Howard) >> 8. Re: Atom numbering in RasMol/Chime -- feature or bug? (Miguel) >> >> --__--__-- >> >> Message: 1 >> Date: Wed, 1 Oct 2003 13:06:44 +0200 (CEST) >> From: "Miguel" <[EMAIL PROTECTED]> >> To: <[EMAIL PROTECTED]> >> Cc: <[EMAIL PROTECTED]> >> Subject: [Jmol-developers] 0-based vs 1-based atom numbering >> >> Hens, >> >> I took a look at the atom numbering in RasMol. >> The heart of the Chime code is based upon RasMol ... so they will be >> the same. >> >> Here is what I found out about the atom numbering: >> with .pdb files the atom number is the number in the file >> with .mol files the atom numbering starts with 1 >> with .xyz files the atom numbering starts with 0 >> >> I am *not* happy about this :-( >> >> Will advise. >> >> Miguel >> >> >> >> >> >> >> >> >> --__--__-- >> >> Message: 2 >> Date: Wed, 1 Oct 2003 13:20:08 +0200 (CEST) >> From: "Miguel" <[EMAIL PROTECTED]> >> To: <[EMAIL PROTECTED]>, <[EMAIL PROTECTED]> >> Cc: <[EMAIL PROTECTED]> >> Subject: [Jmol-developers] Atom numbering in RasMol/Chime -- feature >> or > bug? >> >> Observations and a question regarding atom numbering in RasMol. >> >> atom numbers can be displayed in labels using >> label %i >> >> atoms can be selected by number using >> select atomno=1 >> >> .pdb files have an atom number in the file. This number is used as the >> 'atomno'. >> >> .mol and .xyz files do not have atom numbers in the file. Therefore, >> numbers are assigned sequentially. However: >> for .mol files the atom numbers start with 1 >> for .xyz files the atom numbers start with 0 >> >> (I have not checked it out in Chime, but I assume it is the same). >> >> Question: Is there some rhyme/reason/rationale for this behavior? >> >> >> Miguel >> >> >> >> >> >> >> --__--__-- >> >> Message: 3 >> To: [EMAIL PROTECTED] >> From: "SourceForge.net" <[EMAIL PROTECTED]> >> Date: Wed, 01 Oct 2003 04:53:39 -0700 >> Subject: [Jmol-developers] [ jmol-Bugs-815789 ] What to do about label > fontsize >> >> Bugs item #815789, was opened at 2003-10-01 13:53 >> Message generated for change (Tracker Item Submitted) made by Item > Submitter >> You can respond by visiting: >> > https://sourceforge.net/tracker/?func=detail&atid=379133&aid=815789&group_id > =23629 >> >> Category: None >> Group: None >> Status: Open >> Resolution: None >> Priority: 5 >> Submitted By: Michael T Howard (michaelthoward) >> Assigned to: Michael T Howard (michaelthoward) >> Summary: What to do about label fontsize >> >> Initial Comment: >> How should I handle fontsize to be compatible with existing >> >> RasMol scripts? >> >> >> >> For now, I am going to add 4 to all font sizes ... but this is a >> >> kludge. >> >> >> >> ---------------------------------------------------------------------- >> >> You can respond by visiting: >> > https://sourceforge.net/tracker/?func=detail&atid=379133&aid=815789&group_id > =23629 >> >> >> --__--__-- >> >> Message: 4 >> Date: Wed, 01 Oct 2003 13:06:12 +0100 >> To: <[EMAIL PROTECTED]> >> From: Peter Murray-Rust <[EMAIL PROTECTED]> >> Subject: Re: [Jmol-developers] 0-based vs 1-based atom numbering >> >> At 13:06 01/10/2003 +0200, Miguel wrote: >> >Hens, >> > >> >I took a look at the atom numbering in RasMol. >> >The heart of the Chime code is based upon RasMol ... so they will be >> the same. >> > >> >Here is what I found out about the atom numbering: >> > with .pdb files the atom number is the number in the file >> > with .mol files the atom numbering starts with 1 >> > with .xyz files the atom numbering starts with 0 >> > >> >I am *not* happy about this :-( >> >> This is a tough area because the semantics are fuzzy. Particularly >> where the number is implicit (as in mol, xyz) or has gaps (e.g. PDB). >> It may > help >> to think of these "numbers" as labels. Again it is dangerous to try to >> map to the *internal* numbering in another program because it might >> get > updated >> when you are looking. It is particular problematic when the numbering >> changes when an atom is added/deleted. >> >> In general I would try to use these "numbers" only for input/output or > when >> they have to be visually displayed to a human. If it's feasible I >> would create additional data storage for these number rather than >> trying to keep them in sync. Having to remember when to add +1, etc. >> is fragile >> >> P. >> >> >> >> >> >> >Will advise. >> > >> >Miguel >> > >> > >> > >> > >> > >> > >> > >> > >> >------------------------------------------------------- >> >This sf.net email is sponsored by:ThinkGeek >> >Welcome to geek heaven. >> >http://thinkgeek.com/sf >> >_______________________________________________ >> >Jmol-developers mailing list >> >[EMAIL PROTECTED] >> >https://lists.sourceforge.net/lists/listinfo/jmol-developers >> >> >> >> --__--__-- >> >> Message: 5 >> Date: Wed, 01 Oct 2003 13:10:31 +0100 >> To: <[EMAIL PROTECTED]> >> From: Peter Murray-Rust <[EMAIL PROTECTED]> >> Subject: Re: [Jmol-developers] Atom numbering in RasMol/Chime -- >> feature or bug? >> >> At 13:20 01/10/2003 +0200, Miguel wrote: >> >Observations and a question regarding atom numbering in RasMol. >> > >> >atom numbers can be displayed in labels using >> > label %i >> > >> >atoms can be selected by number using >> > select atomno=1 >> > >> >.pdb files have an atom number in the file. This number is used as >> the 'atomno'. >> >> It will probably (but I suspect not always) be 1 for the first atom. >> >> >> >.mol and .xyz files do not have atom numbers in the file. Therefore, >> numbers are assigned sequentially. However: >> > for .mol files the atom numbers start with 1 >> > for .xyz files the atom numbers start with 0 >> > >> >(I have not checked it out in Chime, but I assume it is the same). >> > >> >Question: Is there some rhyme/reason/rationale for this behavior? >> >> I believe that MDL format had roots in the FORTRAN era and also had to >> be hand hacked by chemists. RasMol was written in C. I can't remember >> about XMol but I suspect it was C. >> >> P. >> >> >> >> >Miguel >> > >> > >> > >> > >> > >> > >> >------------------------------------------------------- >> >This sf.net email is sponsored by:ThinkGeek >> >Welcome to geek heaven. >> >http://thinkgeek.com/sf >> >_______________________________________________ >> >Jmol-developers mailing list >> >[EMAIL PROTECTED] >> >https://lists.sourceforge.net/lists/listinfo/jmol-developers >> >> >> >> --__--__-- >> >> Message: 6 >> Date: Wed, 1 Oct 2003 14:53:15 +0200 (CEST) >> From: "Miguel" <[EMAIL PROTECTED]> >> To: <[EMAIL PROTECTED]> >> Cc: <[EMAIL PROTECTED]> >> Subject: [Jmol-developers] Re: 0-based vs 1-based atom numbering >> >> >> with .mol files the atom numbering starts with 1 >> >> with .xyz files the atom numbering starts with 0 >> > My advise: start numbering with 1, whatever the format. >> Perhaps, but I am reluctant to break existing scripts. >> >> > The number of people that use numbering of XYZ files in a Chime >> script is rather limited, I suspect. >> Well, the people here at the University of Salamanca have a number of >> scripts with .xyz files. >> >> The other thing that .xyz files are used for is animations >> >> > Once the migration has taken place, we have at least a consistent > system. >> In order to have something consistent going forward, perhaps I should >> introduce another 'variable' which would be consistently applied. >> >> I sent a message to the rasmol mailing list ... we'll wait a day and >> see if I receive any responses. >> >> >> Miguel >> >> >> >> >> >> --__--__-- >> >> Message: 7 >> Date: Wed, 1 Oct 2003 14:56:39 +0200 (CEST) >> Subject: Re: [Jmol-developers] 0-based vs 1-based atom numbering From: >> "Miguel Howard" <[EMAIL PROTECTED]> >> To: <[EMAIL PROTECTED]> >> Cc: <[EMAIL PROTECTED]>, <[EMAIL PROTECTED]> >> >> >>Here is what I found out about the atom numbering: >> >> with .pdb files the atom number is the number in the file >> >> with .mol files the atom numbering starts with 1 >> >> with .xyz files the atom numbering starts with 0 >> >> >> >>I am *not* happy about this :-( >> > >> > This is a tough area because the semantics are fuzzy. Particularly >> where >> > the number is implicit (as in mol, xyz) or has gaps (e.g. PDB). It >> may >> > help to think of these "numbers" as labels. >> I agree that this is a good way to think about it. >> >> Internally, I don't use this number for anything. But script writers >> have (and will) use the atom numbers to identify specific atoms. >> > Again it is dangerous to >> > try to map to the *internal* numbering in another program because >> it might get updated when you are looking. It is particular >> problematic when the numbering changes when an atom is >> added/deleted. >> Agreed. >> >> > In general I would try to use these "numbers" only for input/output >> or when they have to be visually displayed to a human. If it's >> feasible I would create additional data storage for these number >> rather than trying to keep them in sync. Having to remember when to >> add +1, etc. is fragile >> yes >> >> Miguel >> >> >> >> >> --__--__-- >> >> Message: 8 >> Date: Wed, 1 Oct 2003 15:00:26 +0200 (CEST) >> Subject: Re: [Jmol-developers] Atom numbering in RasMol/Chime -- >> feature > or bug? >> From: "Miguel" <[EMAIL PROTECTED]> >> To: <[EMAIL PROTECTED]> >> Cc: <[EMAIL PROTECTED]>, <[EMAIL PROTECTED]> >> >> >>.pdb files have an atom number in the file. This number is used as >> the >> >> 'atomno'. >> > It will probably (but I suspect not always) be 1 for the first atom. >> >> I agree ... I think that 'clean' pdb files seem to always start with >> 1. >> >> However, I have seen several .pdb files where people have gone in and >> deleted large chunks of the file ... in order to isolate a particular >> structure. RasMol/Chime work OK with this type of file. If the first >> atom number is 1234 then you can say: >> select atomno=1234 >> >> >> >> >> >> >> >> --__--__-- >> >> _______________________________________________ >> Jmol-developers mailing list >> [EMAIL PROTECTED] >> https://lists.sourceforge.net/lists/listinfo/jmol-developers >> >> >> End of Jmol-developers Digest > > > > ------------------------------------------------------- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > _______________________________________________ > Jmol-developers mailing list > [EMAIL PROTECTED] > https://lists.sourceforge.net/lists/listinfo/jmol-developers -------------------------------------------------- Miguel Howard [EMAIL PROTECTED] c/Pe�a Primera 11-13 esc dcha 6B 37002 Salamanca Espa�a Spain -------------------------------------------------- telefono casa 923 27 10 82 movil 650 52 54 58 -------------------------------------------------- To call from the US dial 9:00 am Pacific US = home 011 34 923 27 10 82 12:00 noon Eastern US = cell 011 34 650 52 54 58 6:00 pm Spain -------------------------------------------------- ------------------------------------------------------- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
