From: Eric M. <em...@mi...> - 2006-02-26 04:16:10
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I have scripted a view by displaying all atoms, then using "restrict not" to subtract atoms, chains, or groups listed in javascript arrays -- "chipping away" at the molecule step by step. The result is a view of a specified subset of the atoms. Now I want to center the remaining visible atoms. But I don't have a convenient way to select them. Is there a command along the lines of "select visible" or "select displayed"? If not, should there be, for convenience? Perhaps it would not be difficult to add? ---- Eric Martz, Professor Emeritus, Dept Microbiology University of Massachusetts, Amherst MA US http://www.umass.edu/molvis/martz |
From: Bob H. <ha...@st...> - 2006-02-26 04:27:28
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as a matter of fact, there is.... in the prototype: http://www.stolaf.edu/people/hansonr/jmol/test/json I added this because it seemed so useful in terms of getting just the atomInfo for the visible: myArray=jmolGetPropertyAsArray("atomInfo","visible") for example. Eric Martz wrote: > I have scripted a view by displaying all atoms, then using "restrict > not" to subtract atoms, chains, or groups listed in javascript arrays > -- "chipping away" at the molecule step by step. The result is a view > of a specified subset of the atoms. > > Now I want to center the remaining visible atoms. But I don't have a > convenient way to select them. > > Is there a command along the lines of "select visible" or "select > displayed"? > > If not, should there be, for convenience? Perhaps it would not be > difficult to add? > > > ---- > Eric Martz, Professor Emeritus, Dept Microbiology > University of Massachusetts, Amherst MA US > http://www.umass.edu/molvis/martz > > > > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking scripting > language > that extends applications into web and mobile media. Attend the live > webcast > and join the prime developer group breaking into this new coding > territory! > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users |
From: Miguel <mi...@jm...> - 2006-02-27 13:24:45
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> as a matter of fact, there is.... in the prototype: > > http://www.stolaf.edu/people/hansonr/jmol/test/json > > I added this because it seemed so useful in terms of getting just > the atomInfo for the visible: > > myArray=3DjmolGetPropertyAsArray(=22atomInfo=22,=22visible=22) > > for example. Be advised that this 'isVisible' flag was designed for internal use only.= More importantly, the concept of 'visible' is not as well-defined as one might think. If this makes it into 'productin' code then we will need to make sure tha= t the concept is well-documented and well-understood. Miguel |
From: Bob H. <ha...@st...> - 2006-02-27 13:45:04
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Miguel wrote: > >Be advised that this 'isVisible' flag was designed for internal use only. >More importantly, the concept of 'visible' is not as well-defined as one >might think. > >If this makes it into 'production' code then we will need to make sure that >the concept is well-documented and well-understood. > > > > Sure. I agree. It would go under the category of "atom expressions". Please say more, Miguel. Perhaps what "visible" means. Currently, I think, it means: (1) the atom is in a displayed frame and (2) the atom has at least one of the following: a. spacefill > 0 b. wireframe > 0 c. a halo highlight Note that cartoons and such do NOT constitute visible, because they are not atoms. When you have: select * wireframe off;spacefill off; cartoon on select visible you get: 0 atoms selected The only secondary structural visualization that constitutes visible is "backbone", which is really a wireframe connection between alpha carbons in a protein or (what?) in a nucleic acid. So select * wireframe off;spacefill off; backbone on select visible gives you (for 1crn.pdb): 46 atoms selected More to know? Bob |
From: Miguel <mi...@jm...> - 2006-02-27 14:24:31
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> Miguel wrote: > >> >>Be advised that this 'isVisible' flag was designed for internal use onl= y. >>More importantly, the concept of 'visible' is not as well-defined as on= e >>might think. >> >>If this makes it into 'production' code then we will need to make sure >> that >>the concept is well-documented and well-understood. >> >> > Sure. I agree. It would go under the category of =22atom expressions=22= . > Please say more, Miguel. The internal 'isVisible' flag was designed for the 'hover' and to detect which atoms are selected based upon 'clicking' behavior. It could very easily be the case that when atoms are not currently displayed on the screen (because they are zoomed or translated) then the atoms are not 'visible'. I don't remember. > Perhaps what =22visible=22 means. Currently, I > think, it means: > > (1) the atom is in a displayed frame Yes, that is the way that the 'isVisible' flag works ... but I am not sur= e that is the desired behavior for the 'visible' set. > and > > (2) the atom has at least one of the following: > > a. spacefill > 0 > b. wireframe > 0 > c. a halo highlight > > Note that cartoons and such do NOT constitute visible, because they are= > not atoms. I am not sure that is completely true. There may be other schematic representations where the atoms are considered visible. I don't remember.= > When you have: > > select * > wireframe off;spacefill off; cartoon on > select visible > > you get: > > 0 atoms selected > > The only secondary structural visualization that constitutes visible is= > =22backbone=22, which is really > a wireframe connection between alpha carbons in a protein or (what?) Phosphorus or chain-terminating Oxygen. > in a nucleic acid. So > > select * > wireframe off;spacefill off; backbone on > select visible > > gives you (for 1crn.pdb): > > 46 atoms selected > > > More to know? I think that we would be better off reimplementing the 'visible' set to explicitly be the things that you want it to be. That way, it will be well-defined and will not get messed up if/when someone works on some other part of the code. In addition, this will also avoid the confusion associated with whether o= r not the frame was repainted. Finally, I don't think that the 'visible' set should have an implicit restriction based upon the currently displayed frame. No other sets behav= e that way. I think I would be more in favor of a 'visible' set that includes all atoms in all models. If necessary, then we could add another= set which represented all atoms in the currently displayed models. One could AND the two sets together to get the currently visible atoms. Miguel |
From: Bob H. <ha...@st...> - 2006-02-27 14:56:29
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I will investigate this fully and get back to all. Bob -- 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: Clifford F. <cli...@we...> - 2006-03-01 15:03:31
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Dear Miguel and the jmol user and developer community. More and more sites are looking to use your wonderful program. I am pleased to announce that my protein dipole moment server at http://bioinfo.weizmann.ac.il/dipol/indexj.html now uses jmol to display both the protein as a backbone ribbon and the dipole vector in jmol. I am grateful to Dr. Jaime Prilusky for his tremendous help to make this happen. Sincerely, Clifford Felder <cli...@we...> |
From: Rolf H. <rh...@fl...> - 2006-03-01 16:11:44
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Clifford Felder wrote: >Dear Miguel and the jmol user and developer community. More and more sites are >looking to use your wonderful program. I am pleased to announce that my protein >dipole moment server at http://bioinfo.weizmann.ac.il/dipol/indexj.html now >uses jmol to display both the protein as a backbone ribbon and the dipole >vector in jmol. I am grateful to Dr. Jaime Prilusky for his tremendous help to >make this happen. > I looked at it with example code '2arc' and wondered why there appeared 2 Jmol applets, when I opened the larger Jmol view window. If this is intentional I would propose that you at least separate them a bit. Right now they look like one long applet instead of two quadratic ones in my browser (Firefox 1.0.7, SuSE Linux 9.3). Regards, Rolf |
From: Jaime P. <Jai...@we...> - 2006-03-02 06:02:25
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Dear Rolf, Thank you for pointing out this strange behaviour on the large Jmol screen. It also happens on Firefox 1.0.6 on Mac OSX (no javaplugin). The Zoom popup works perfect on Safari on Mac. Maybe I should restrict the Zoom window only to Jmol Supported Browsers. Jaim According to Rolf Huehne: > I looked at it with example code '2arc' and wondered why there appeared > 2 Jmol applets, when I opened the larger Jmol view window. If this is > intentional I would propose that you at least separate them a bit. Right > now they look like one long applet instead of two quadratic ones in my > browser (Firefox 1.0.7, SuSE Linux 9.3). -- Dr Jaime Prilusky | Jai...@we... Head of Bioinformatics ISPC | R&D Bioinformatics and Data Management | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 info URL http://bip.weizmann.ac.il/staff/jaime_prilusky.html OCA is at http://bip.weizmann.ac.il/oca/ |
From: Miguel <mi...@jm...> - 2006-03-01 16:16:46
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Clifford Felder wrote: > I am pleased to announce that my protein dipole moment > server at http://bioinfo.weizmann.ac.il/dipol/indexj.html > now uses jmol to display both the protein as a backbone > ribbon and the dipole vector in jmol. Excellent=21 Miguel |
From: Angel H. <ang...@ua...> - 2006-02-27 14:08:12
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El 27 Feb 2006 a las 7:47, Bob Hanson escribi=F3: > The only secondary structural visualization that constitutes visible is > "backbone", which is really > a wireframe connection between alpha carbons in a protein or (what?) in Phosphorus atoms in a nucleic acid. > a nucleic acid. So > > select * > wireframe off;spacefill off; backbone on > select visible > > gives you (for 1crn.pdb): > > 46 atoms selected I guess those 46 atoms are the alpha carbons. Right? |
From: Eric M. <em...@mi...> - 2006-02-26 17:51:58
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At 2/25/06, you wrote: >as a matter of fact, there is.... in the prototype: > >http://www.stolaf.edu/people/hansonr/jmol/test/json > >I added this because it seemed so useful in terms of getting just >the atomInfo for the visible: > >myArray=jmolGetPropertyAsArray("atomInfo","visible") > >for example. Thanks, Bob. I agree that this is very useful. However, if I understand what you are telling me, it is not "select visible". I would have to write a javascript loop to construct select commands from the myArray, as I understand it. I still think that "select visible", as a command built into Jmol, might be a very worthwhile addition to the command set. -Eric |
From: Bob H. <ha...@st...> - 2006-02-27 01:52:48
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Eric Martz wrote: > At 2/25/06, you wrote: > >> as a matter of fact, there is.... in the prototype: >> >> http://www.stolaf.edu/people/hansonr/jmol/test/json >> > it is, in fact, select visible "visible" is now a selectable token, like "helix" or "carbon" Try it out at http://www.stolaf.edu/people/hansonr/jmol/test/json/property.htm You can say: select visible and not carbon select within(2.0, oxygen) and not visible select within(2.0, visible) etc. That way it can also be used in jmolGetPropertyAsArray("atomInfo","visible") because that second parameter is just anything that can be selected. Should do the trick, right? Bob |
From: Eric M. <em...@mi...> - 2006-02-27 02:32:35
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At 2/26/06, Bob Hanson wrote: >it is, in fact, > >select visible > >[snip] >Should do the trick, right? You bet, Bob. Outstanding! -Eric |
From: Bob H. <ha...@st...> - 2006-02-27 02:49:59
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a pleasure. ooooh, I see center visible is especially nice! Eric Martz wrote: > At 2/26/06, Bob Hanson wrote: > >> it is, in fact, >> >> select visible >> >> [snip] > > >> Should do the trick, right? > > > > You bet, Bob. Outstanding! -Eric > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking scripting > language > that extends applications into web and mobile media. Attend the live > webcast > and join the prime developer group breaking into this new coding > territory! > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users |
From: Bob H. <ha...@st...> - 2006-02-27 12:27:48
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Eric, I just added one fix to "visible" that you are going to tell me I need to do today. :) In general Jmol waits until the end of a script to "refresh" the model. It is at this refreshing point when what is visible and what is not is determined. Thus, the command: restrict carbon; select visible; would not necessarily work as expected. (The other atoms might still be "visible" until after the script completes.) I've checked in changes that fix this; jar files are available in http://www.stolaf.edu/people/hansonr/jmol/test/json Bob Eric Martz wrote: > At 2/26/06, Bob Hanson wrote: > >> it is, in fact, >> >> select visible >> >> [snip] > > >> Should do the trick, right? > > > > You bet, Bob. Outstanding! -Eric > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking scripting > language > that extends applications into web and mobile media. Attend the live > webcast > and join the prime developer group breaking into this new coding > territory! > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users |
From: Miguel <mi...@jm...> - 2006-02-27 13:26:06
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> I still think that =22select visible=22, as a command built into Jmol, = might > be > a very worthwhile addition to the command set. Please define 'visible' ... as you see it :-) Miguel |