From: Alexander R. <ale...@we...> - 2014-01-17 14:09:08
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Hi Bob, any chance you could add a "displayed" atom property like the "selected" atom property? Best Alexander |
From: Herráez S. Á. <ang...@ua...> - 2014-01-17 14:31:03
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Alexander, Maybe`visible` does what you need? ________________________________________ De: Alexander Rose [ale...@we...] Enviado: viernes, 17 de enero de 2014 15:08 Para: Jmol Developers Asunto: [Jmol-developers] feature request: "displayed" atom property Hi Bob, any chance you could add a "displayed" atom property like the "selected" atom property? Best Alexander ------------------------------------------------------------------------------ CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments & Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk _______________________________________________ Jmol-developers mailing list Jmo...@li... https://lists.sourceforge.net/lists/listinfo/jmol-developers |
From: Robert H. <ha...@st...> - 2014-01-17 16:17:27
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That's there. select displayed delete !displayed print {displayed} all working. Hmm... Difference between that and VISIBLE.... On Fri, Jan 17, 2014 at 9:08 AM, Alexander Rose <ale...@we... > wrote: > Hi Bob, > > any chance you could add a "displayed" atom property like the "selected" > atom property? > > > Best > Alexander > > > ------------------------------------------------------------------------------ > CenturyLink Cloud: The Leader in Enterprise Cloud Services. > Learn Why More Businesses Are Choosing CenturyLink Cloud For > Critical Workloads, Development Environments & Everything In Between. > Get a Quote or Start a Free Trial Today. > > http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Robert H. <ha...@st...> - 2014-01-17 16:23:57
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case T.displayed: rpn.addXBs(BSUtil.copyInvert(viewer.getHiddenSet(), atomCount)); break; case T.visible: if (!chk && !refreshed) viewer.setModelVisibility(); refreshed = true; rpn.addXBs(viewer.getVisibleSet()); break; So displayed is just what is not hidden. Visible is a bit different. With proteins, any atom in a group that is shown with a cartoon (for instance) is "visible" even though it is not a ball or star itself. But I think there is a bug there. I'm seeing visible even for a small molecule with balls and sticks turned off. On Fri, Jan 17, 2014 at 11:17 AM, Robert Hanson <ha...@st...> wrote: > That's there. > > select displayed > delete !displayed > print {displayed} > > all working. > > Hmm... Difference between that and VISIBLE.... > > > > > > On Fri, Jan 17, 2014 at 9:08 AM, Alexander Rose < > ale...@we...> wrote: > >> Hi Bob, >> >> any chance you could add a "displayed" atom property like the "selected" >> atom property? >> >> >> Best >> Alexander >> >> >> ------------------------------------------------------------------------------ >> CenturyLink Cloud: The Leader in Enterprise Cloud Services. >> Learn Why More Businesses Are Choosing CenturyLink Cloud For >> Critical Workloads, Development Environments & Everything In Between. >> Get a Quote or Start a Free Trial Today. >> >> http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk >> _______________________________________________ >> Jmol-developers mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-developers >> > > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Angel H. <ang...@ua...> - 2014-01-17 16:46:37
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> Visible is a bit different. With proteins, any atom in a group that > is shown with a cartoon (for instance) is "visible" even though it is > not a ball or star itself. So is e.g. a beta carbon in an amino acid displayed as cartoon only. Is that also "displayed" ? I'd expect all atoms in a residue would be "displayed" if the residue has not been hidden, irrespective of the rendering style. Should it then be "visible" or not? I'm not expressing a preference, just I'm not sure what is the expected behaviour. If asked, I would have said they were synonymous --but never tried it. |
From: Robert H. <ha...@st...> - 2014-01-17 16:50:26
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On Fri, Jan 17, 2014 at 11:46 AM, Angel Herráez <ang...@ua...>wrote: > > Visible is a bit different. With proteins, any atom in a group that > > is shown with a cartoon (for instance) is "visible" even though it is > > not a ball or star itself. > > So is e.g. a beta carbon in an amino acid displayed as cartoon only. > > Is that also "displayed" ? > > yes. DISPLAYED is specifically what you have indicated are not to be hidden. $ load "c:/jmol-dev/bobtest/cyclohexane_movie.xyz" 35 models $ select displayed 630 atoms selected $ select visible 18 atoms selected Definitely not the same thing. As I said, there is a bug: load $C\C=C\CC select _C wireframe off spacefill off display !_H select visible // 5 (but nothing is showing) That's a bug that probably goes back to 2006. > > > > > > > > > ------------------------------------------------------------------------------ > CenturyLink Cloud: The Leader in Enterprise Cloud Services. > Learn Why More Businesses Are Choosing CenturyLink Cloud For > Critical Workloads, Development Environments & Everything In Between. > Get a Quote or Start a Free Trial Today. > > http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Angel H. <ang...@ua...> - 2014-01-17 16:48:21
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Hmmm... Alexander was asking about an atom property, not an atomset El 17 Jan 2014 a las 11:17, Robert Hanson escribió: > select displayed > delete !displayed > print {displayed} |
From: Robert H. <ha...@st...> - 2014-01-17 16:51:52
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Oh, you mean xxx.displayed xxx.selected sure. I missed that! On Fri, Jan 17, 2014 at 11:48 AM, Angel Herráez <ang...@ua...>wrote: > Hmmm... > Alexander was asking about an atom property, not an atomset > > El 17 Jan 2014 a las 11:17, Robert Hanson escribió: > > select displayed > > delete !displayed > > print {displayed} > > > > ------------------------------------------------------------------------------ > CenturyLink Cloud: The Leader in Enterprise Cloud Services. > Learn Why More Businesses Are Choosing CenturyLink Cloud For > Critical Workloads, Development Environments & Everything In Between. > Get a Quote or Start a Free Trial Today. > > http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Robert H. <ha...@st...> - 2014-01-17 17:01:22
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I'd rather not go down that route -- there are plenty of properties like that -- selected, displayed, hidden, clickable. Where would it end? Certainly for a given atom *a* you can do this: if ({a and displayed}) {....} or you can do this for (a in {displayed}) {....} So I guess you could do this: for (a in {displayed}) a.property_displayed = 1 I think that's your best bet. On Fri, Jan 17, 2014 at 9:08 AM, Alexander Rose <ale...@we... > wrote: > Hi Bob, > > any chance you could add a "displayed" atom property like the "selected" > atom property? > > > Best > Alexander > > > ------------------------------------------------------------------------------ > CenturyLink Cloud: The Leader in Enterprise Cloud Services. > Learn Why More Businesses Are Choosing CenturyLink Cloud For > Critical Workloads, Development Environments & Everything In Between. > Get a Quote or Start a Free Trial Today. > > http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Alexander R. <ale...@we...> - 2014-01-17 17:44:54
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Hi, ----- Ursprüngliche Mail ----- > Von: "Robert Hanson" <ha...@st...> > > I'd rather not go down that route -- there are plenty of properties > like that -- selected, displayed, hidden, clickable. Where would it > end? > Ok, understandable. I'll work around it. Tanks. Best Alexander > Certainly for a given atom a you can do this: > > if ({a and displayed}) {....} > > or you can do this > > for (a in {displayed}) {....} > > So I guess you could do this: > > for (a in {displayed}) a.property_displayed = 1 > > > > I think that's your best bet. > > > > > > > > On Fri, Jan 17, 2014 at 9:08 AM, Alexander Rose < > ale...@we... > wrote: > > > Hi Bob, > > any chance you could add a "displayed" atom property like the > "selected" atom property? > > > Best > Alexander > > ------------------------------------------------------------------------------ > CenturyLink Cloud: The Leader in Enterprise Cloud Services. > Learn Why More Businesses Are Choosing CenturyLink Cloud For > Critical Workloads, Development Environments & Everything In Between. > Get a Quote or Start a Free Trial Today. > http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > > > -- > > Robert M. Hanson > Larson-Anderson Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > ------------------------------------------------------------------------------ > CenturyLink Cloud: The Leader in Enterprise Cloud Services. > Learn Why More Businesses Are Choosing CenturyLink Cloud For > Critical Workloads, Development Environments & Everything In Between. > Get a Quote or Start a Free Trial Today. > http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > |