From: <spi...@ma...> - 2008-08-30 15:42:07
|
This is a preliminary inquiry about two feature requests. In my MolnIquiry site, I have imbedded line objects as bonds that can then be ?picked?; for example, students are asked to click on a peptide bond.). Creating these objects is a task, particularly if many are needed, and the lines can become visible if wireframe is turned off. Is it technically feasible that Jmol could: 1. generate a series of IDed objects between the connected atoms of an atom set e.g.: ?select (atom expression), drawConnected line, ID ?line?+j? where j is incrementally increased with each line? 2. set the color of an object as ?transparent? (but still pickable). Does anyone see any other applications of these features? Thanks. Steve Dept of Biology and Environmental Science Marietta College ---------------------------------------------------------------- This message was sent using Marietta College WebMail. |
From: Robert H. <ha...@st...> - 2008-08-30 18:11:43
|
Steve, there's probably not much sense in creating a generic bond-equivalent object like that. But you can do what you say yourself. For example, if a student is asked to click on a peptide bond, you know what bond it is, so you can create the link yourself and, like you say, make them transparent but still clickable. That you can do right now. But I see your point about lots of these. I don't see why we can't set up bond picking if that is what you are after. Wouldn't that be better? Bob On Sat, Aug 30, 2008 at 10:41 AM, spi...@ma... < spi...@ma...> wrote: > This is a preliminary inquiry about two feature requests. In my > MolnIquiry site, I have imbedded line objects as bonds that can then be > ?picked?; for example, students are asked to click on a peptide bond.). > Creating these objects is a task, particularly if many are needed, and the > lines can become visible if wireframe is turned off. > > Is it technically feasible that Jmol could: > > 1. generate a series of IDed objects between the connected atoms of an > atom set e.g.: ?select (atom expression), drawConnected line, ID ?line?+j? > > where j is incrementally increased with each line? > > 2. set the color of an object as ?transparent? (but still pickable). > > Does anyone see any other applications of these features? > > Thanks. > > Steve > > Dept of Biology and Environmental Science > > Marietta College > > > ---------------------------------------------------------------- > This message was sent using Marietta College WebMail. > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson 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...> - 2008-08-30 19:20:29
|
Jmol 11.6.RC12 now has set atomPicking [default TRUE] set bondPicking [default FALSE] The report from the bond picking looks like this: ["bond","69 1 [GLY]37.C #263 -- [GLY]37.CA #262 1.5251089",21.2975,16.2235,6.4700003] The First number is the bond ID. It is the number you would use to get the bond properties: print getProperty("BondInfo[69]") or print getproperty("BondInfo", 69) This number is also one more than the number you would use to specify that bond using bond set notation (because in that case 0 is the first bond): select [{68}]; color BOND white The number 1 is the bond order; next are the identities of the two atoms and the bond distance. The last three numbers are the coordinates of the center of the bond. That work for you, Steve? Bob On Sat, Aug 30, 2008 at 1:11 PM, Robert Hanson <ha...@st...> wrote: > Steve, there's probably not much sense in creating a generic > bond-equivalent object like that. But you can do what you say yourself. For > example, if a student is asked to click on a peptide bond, you know what > bond it is, so you can create the link yourself and, like you say, make them > transparent but still clickable. That you can do right now. But I see your > point about lots of these. I don't see why we can't set up bond picking if > that is what you are after. Wouldn't that be better? > > Bob > > > On Sat, Aug 30, 2008 at 10:41 AM, spi...@ma... < > spi...@ma...> wrote: > >> This is a preliminary inquiry about two feature requests. In my >> MolnIquiry site, I have imbedded line objects as bonds that can then be >> ?picked?; for example, students are asked to click on a peptide bond.). >> Creating these objects is a task, particularly if many are needed, and the >> lines can become visible if wireframe is turned off. >> >> Is it technically feasible that Jmol could: >> >> 1. generate a series of IDed objects between the connected atoms of an >> atom set e.g.: ?select (atom expression), drawConnected line, ID ?line?+j? >> >> where j is incrementally increased with each line? >> >> 2. set the color of an object as ?transparent? (but still pickable). >> >> Does anyone see any other applications of these features? >> >> Thanks. >> >> Steve >> >> Dept of Biology and Environmental Science >> >> Marietta College >> >> >> ---------------------------------------------------------------- >> This message was sent using Marietta College WebMail. >> >> ------------------------------------------------------------------------- >> This SF.Net email is sponsored by the Moblin Your Move Developer's >> challenge >> Build the coolest Linux based applications with Moblin SDK & win great >> prizes >> Grand prize is a trip for two to an Open Source event anywhere in the >> world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > -- > Robert M. Hanson > 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 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: A. H. <ang...@ua...> - 2008-08-30 19:38:05
|
On 30 Aug 2008 at 14:20, Robert Hanson wrote: > Jmol 11.6.RC12 now has > > set atomPicking [default TRUE] > set bondPicking [default FALSE] Nice! and quick Are those 2 independently set, or are they alternative options? And, how does that combine with the different "set picking" variants? |
From: Robert H. <ha...@st...> - 2008-08-30 20:08:10
|
all three are independent: set atomPicking set bondPicking set drawPicking On Sat, Aug 30, 2008 at 2:49 PM, Angel Herráez <ang...@ua...> wrote: > On 30 Aug 2008 at 14:20, Robert Hanson wrote: > > Jmol 11.6.RC12 now has > > > > set atomPicking [default TRUE] > > set bondPicking [default FALSE] > > > Nice! and quick > Are those 2 independently set, or are they alternative options? > > And, how does that combine with the different "set picking" variants? > > > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson 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 |