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
