From: Frieda R. <fr...@ns...> - 2005-08-27 22:26:04
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Is there a way to limit the number of decimal places shown next to monitor lines? I would like only one (can't find this documented, if it is please let me know). Frieda |
From: Miguel <mi...@jm...> - 2005-08-29 02:50:50
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> Is there a way to limit the number of decimal places shown next to > monitor lines? I would like only one (can't find this documented, if it= > is please let me know). There is currently no mechanism to support this. Miguel |
From: Frieda R. <fr...@ns...> - 2005-08-30 14:25:17
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>> Is there a way to limit the number of decimal places shown next to >> monitor lines? I would like only one (can't find this documented, if >> it >> is please let me know). On Aug 28, 2005, at 10:50 PM, Miguel wrote: > There is currently no mechanism to support this. If this is not too difficult to implement, I would find it very useful to be able to round off the decimals to one place. In cases where you are indicating several nearby measurements in one structure, they wind up obscuring the structure itself. In addition, at least for angstroms I think the additional decimal places may not be significant. Any hope for this feature request? Frieda |
From: Miguel <mi...@jm...> - 2005-08-30 16:02:41
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When displaying distance measurements ... Q: Does anyone feel the need to have more than one digit to the right of the decimal point when measuring in Angstroms? (or 2 digits with nanometers) Example: 1.234 A -> 1.2 A 0.1234 nm -> 0.12 nm If you are in favor of having more than one digit ... Q: Are you sure that showing extra digits is not implying some false leve= l of precision? > If this is not too difficult to implement, I would find it very useful > to be able to round off the decimals to one place. In cases where you > are indicating several nearby measurements in one structure, they wind > up obscuring the structure itself. In addition, at least for angstroms > I think the additional decimal places may not be significant. Any hope > for this feature request? I made an executive decision to reduce the number of digits to the right of the decimal place by one. So now picometers are shown as integers and angstroms are shown with two digits to the right of the decimal point. Let's see what other people think. Miguel |
From: Bob H. <ha...@st...> - 2005-08-30 16:08:01
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I like this but prefer one digit to the right for Angstroms. I do not understand why the default units is nm instead of Angstroms or pm. This seems very strange to me. My experience is that nm are only used in spectroscopy. Bob Miguel wrote: > I made an executive decision to reduce the number of digits to the right > of the decimal place by one. So now picometers are shown as integers and > angstroms are shown with two digits to the right of the decimal point. > -- Robert M. Hanson, ha...@st..., 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:ha...@st... http://www.stolaf.edu/people/hansonr "Imagination is more important than knowledge." - Albert Einstein |
From: Miguel <mi...@jm...> - 2005-08-30 16:23:44
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> I like this but prefer one digit to the right for Angstroms. If noone makes a strong argument to the contrary then we will change it t= o one digit. > I do not understand why the default units is nm > instead of Angstroms or pm. > This seems very strange to me. > My experience is that nm are only used in spectroscopy. I was told that: - the Royal Chemical Society mandates that everything be done in nanomet= ers - many publications no longer accept angstroms - angstroms are not even taught in European schools Those sounded like very good reasons to me. I am quite sure there was some discussion of this on the mailing list before I changed it. Miguel |
From: <rg...@el...> - 2005-08-30 17:03:18
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On Tue, August 30, 2005 12:22 pm, Miguel said: > > I was told that: > > - the Royal Chemical Society mandates that everything be done in > nanometers For molecular structures the standard SI unit would be pm. > - many publications no longer accept angstroms Not that I am aware of. All the journals that accept crystallographic results will accept pm but prefer Angstroms. The CIF default is Angstroms (mandated by the International Union of Crystallography. > - angstroms are not even taught in European schools That may be true. Rich |
From: Hens B. <h.b...@cm...> - 2005-08-30 20:16:47
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Miguel wrote: >>I like this but prefer one digit to the right for Angstroms. >> >> > >If noone makes a strong argument to the contrary then we will change it to >one digit. > > > I support Rich in that one digit (in Angstroms) is too few for comparing bond lengths in organic structures, two is the minimum, three is mostly used in cartesian coordinates. (Ever seen cartesian coordinates in pm or nm?) Hens |
From: Eric M. <em...@mi...> - 2005-09-01 19:27:54
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I vote (somewhat belatedly): A. That the default unit for distance in jmol be Angstroms. B. That the default precision be two digits following the decimal point. See further discussion below. At 8/30/05, Miguel wrote: > > I do not understand why the default units is nm > > instead of Angstroms or pm. > > This seems very strange to me. > > My experience is that nm are only used in spectroscopy. > >I was told that: > > - the Royal Chemical Society mandates that everything be done in nanometers > - many publications no longer accept angstroms > - angstroms are not even taught in European schools > >Those sounded like very good reasons to me. And indeed they do sound that way, but (sorry Miguel) I can't resist saying ... and I was told that: 1. The USA is converting to metric units (I was told that several decades ago). But even road signs are still not in km. More signs are in Spanish (a good thing!) than in metric. 2. mmCIF is the new standard for protein structure data. But in fact nearly all crystallographers still prepare and submit their data in PDB format, and nearly all protein structure software uses PDB format (often exclusively). My impression is that Angstroms are the preferred unit among protein crystallographers, regardless of the official line. |
From: Miguel <mi...@jm...> - 2005-09-01 21:11:51
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> I vote (somewhat belatedly): > > A. That the default unit for distance in jmol be Angstroms. no comment at this time > B. That the default precision be two digits following the decimal point= . This has been changed to two. There is currently no syntax to allow the user to change the precision ..= . I need to come up with some way to extend the command set measurements angstroms=7Cnanometers=7Cpicometers <precision> Miguel |
From: Jan R. <jo...@gm...> - 2005-09-02 08:16:30
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Miguel wrote: >> I vote (somewhat belatedly): >> >> A. That the default unit for distance in jmol be Angstroms. >> > > me too, but I've no problem with adding set measurements angstroms set chainCaseSensitive off set ribbonedge on background white select carbon color green ... to a startup script. > no comment at this time > > >> B. That the default precision be two digits following the decimal point. >> > > This has been changed to two. > why not calculating precision dynamically from the source coordinate precision? Regards, Jan > There is currently no syntax to allow the user to change the precision ... > I need to come up with some way to extend the command > > set measurements angstroms|nanometers|picometers <precision> > |
From: Bob H. <ha...@st...> - 2005-09-02 12:00:41
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Jan Reichert wrote: > why not calculating precision dynamically from the source coordinate > precision? Brilliant! -- Robert M. Hanson, ha...@st..., 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:ha...@st... http://www.stolaf.edu/people/hansonr |
From: <rg...@el...> - 2005-08-30 16:17:34
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On Tue, August 30, 2005 12:01 pm, Miguel said: > When displaying distance measurements ... > > Q: Does anyone feel the need to have more than one digit to the right of > the decimal point when measuring in Angstroms? (or 2 digits with > nanometers) [snip] > > I made an executive decision to reduce the number of digits to the right > of the decimal place by one. So now picometers are shown as integers and > angstroms are shown with two digits to the right of the decimal point. > If I were requesting the feature I'd want it to be user-selectable for 1,2 or 3 decimal places for Angstrom units. For some very well-determined structures (that are small enough for easy display/viewing) it might be useful to see the distances to their full (i.e. thousandths) precision. Tenths of Angstroms is of use only for the grossest of comparisons, hundredths would be the minimum for scientific usefulness. Rich |
From: Egon W. <e.w...@sc...> - 2005-08-30 17:29:18
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On Tuesday 30 August 2005 18:22, Miguel wrote: > I was told that: > - the Royal Chemical Society mandates that everything be done in > nanometers > - many publications no longer accept angstroms I remember a discussion on this on the list. But cannot find it with Google. Conclusion indeed was that angstrom where to be phased out. > - angstroms are not even taught in European schools At our university we did, but angstrom is indeed a non-standard distance measured and deprecated, though still often used. > Those sounded like very good reasons to me. Agreed. But it's switchable anyway, right? > I am quite sure there was some discussion of this on the mailing list > before I changed it. Confirmed (see above). Egon -- e.w...@sc... PhD student on Molecular Representation in Chemometrics Radboud University Nijmegen http://www.cac.science.ru.nl/people/egonw/ GPG: 1024D/D6336BA6 |
From: <rg...@el...> - 2005-08-30 17:45:58
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On Tue, August 30, 2005 1:29 pm, Egon Willighagen said: > > I remember a discussion on this on the list. But cannot find it with > Google. Last August. > Conclusion indeed was that angstrom where to be phased out. Not quite. Angstrom measurements are deprecated in all aspects other than crystallography with nm or pm preferred in those other fields. The majority of the on-list comments were in favour of an Angstrom default. Rich |
From: Egon W. <e.w...@sc...> - 2005-08-30 17:54:32
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On Tuesday 30 August 2005 19:45, rg...@el... wrote: > On Tue, August 30, 2005 1:29 pm, Egon Willighagen said: > > I remember a discussion on this on the list. But cannot find it with > > Google. > > Last August. Indeed [1]. Thanx. > > Conclusion indeed was that angstrom where to be phased out. > > Not quite. Angstrom measurements are deprecated in all aspects other than > crystallography with nm or pm preferred in those other fields. The > majority of the on-list comments were in favour of an Angstrom default. Right [2]. Egon 1. http://sourceforge.net/mailarchive/forum.php?forum_id=2151&max_rows=25&offset=25&style=ultimate&viewmonth=200408 2. http://sourceforge.net/mailarchive/forum.php?thread_id=5348298&forum_id=2151 -- e.w...@sc... PhD student on Molecular Representation in Chemometrics Radboud University Nijmegen http://www.cac.science.ru.nl/people/egonw/ GPG: 1024D/D6336BA6 |