From: Thomas S. <tho...@gm...> - 2008-07-25 17:03:14
|
Hi everyone -- I have a script that iterates over a range of residues that is defined by choosing the "min" and "max" residue numbers. When testing out version 11.5.49 in order to take advantage of some of the great new additions, I find that the line in my script with "max" is throwing errors...specifically: select ligand; nAtoms= {selected}.size; rx = {selected}.resno.min; ry = {selected}.resno.max; for (var i=rx;i<=ry;i=i+1) ETC and here is the resulting error: 84 atoms selected script ERROR: unrecognized atom property: 0x300092 ----line 4 command 4 of file null: ry = { selected } . resno . >> max << This happens both from my script and when entering the commands into the console. BTW, I am using the applet in a web page.... I would expect that I've created my own mistake, but this does work as written in version 11.5.37..... Thoughts? Thanks, Tom |
From: Bob H. <ha...@st...> - 2008-07-25 23:40:14
|
yes. ARGH! I know exactly what I did.... Thanks for spotting that. I will have an update available later this evening. Bob Thomas Stout wrote: > > Hi everyone -- > > I have a script that iterates over a range of residues that is defined > by choosing the "min" and "max" residue numbers. When testing out > version 11.5.49 in order to take advantage of some of the great new > additions, I find that the line in my script with "max" is throwing > errors...specifically: > > select ligand; > nAtoms= {selected}.size; > rx = {selected}.resno.min; > ry = {selected}.resno.max; > > for (var i=rx;i<=ry;i=i+1) > ETC > > and here is the resulting error: > > 84 atoms selected > script ERROR: unrecognized atom property: 0x300092 > ----line 4 command 4 of file null: > ry = { selected } . resno . >> max << > > This happens both from my script and when entering the commands into > the console. BTW, I am using the applet in a web page.... > I would expect that I've created my own mistake, but this does work as > written in version 11.5.37. <http://11.5.37.>.... > > Thoughts? > > Thanks, > Tom > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >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: Thomas S. <tho...@gm...> - 2008-07-26 01:24:49
|
Thanks for the quick fix Bob! I'll try it out as soon as I can get the new files... -Tom On Fri, Jul 25, 2008 at 4:40 PM, Bob Hanson <ha...@st...> wrote: > yes. ARGH! I know exactly what I did.... Thanks for spotting that. I > will have an update available later this evening. > > Bob > > Thomas Stout wrote: > > > > > Hi everyone -- > > > > I have a script that iterates over a range of residues that is defined > > by choosing the "min" and "max" residue numbers. When testing out > > version 11.5.49 in order to take advantage of some of the great new > > additions, I find that the line in my script with "max" is throwing > > errors...specifically: > > > > select ligand; > > nAtoms= {selected}.size; > > rx = {selected}.resno.min; > > ry = {selected}.resno.max; > > > > for (var i=rx;i<=ry;i=i+1) > > ETC > > > > and here is the resulting error: > > > > 84 atoms selected > > script ERROR: unrecognized atom property: 0x300092 > > ----line 4 command 4 of file null: > > ry = { selected } . resno . >> max << > > > > This happens both from my script and when entering the commands into > > the console. BTW, I am using the applet in a web page.... > > I would expect that I've created my own mistake, but this does work as > > written in version 11.5.37. <http://11.5.37.>.... > > > > Thoughts? > > > > Thanks, > > Tom > > > >------------------------------------------------------------------------ > > > >------------------------------------------------------------------------- > >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 > > > > ------------------------------------------------------------------------- > 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 > |
From: Bob H. <ha...@st...> - 2008-07-26 00:22:50
|
11.5.49 and 11.5.50 are broken for ".max" (.min is OK) This is fixed for 11.5.51 -- Nico, if you would please release that. Files are also available in http://chemapps.stolaf.edu/jmol/docs/examples-11 Also new for 11.5.51, while I am at it... CIF BETAij anisotropic support -- preliminary -- totally untested correct implementation of set axisOrientationRasmol. (inverted Y axis; default position rotated 180 degrees about X) slightly different axis labels for set axesmolecular TRUE (+x, +y, +z) or FALSE (x, y, z) or axisOrientationRasmol -- x, (y), z The Jmol application has a set of buttons in the toolbar across the top of the window -- rotate, select, and measure. As far as I can tell, these were never implemented. They are now. Click the pointer (select) to select atoms using SHIFT-LEFT dragging the mouse to display a selection box. (Not tested on Macs.) The algorithm uses the "tog" function -- select selected tog {...what you select by dragging...} That's not in the documentation, I think. "tog" stands for "toggle". A tog B = (not A) if A == B A tog B = (A or B) if A != B Mostly, I don't recommend using tog! But in this case tog 1) selects everything that is in the selection box if none of the atoms are selected already. 2) selects everything not already selected if some but not all of the atoms are selected already. 3) does a NOT operation if all atoms are already selected. Believe it or not, that's pretty intuitive. The more you select, the more atoms are included, but if you select a set of atoms that are already all selected, then those atoms are unselected. Bob Thomas Stout wrote: > > Hi everyone -- > > I have a script that iterates over a range of residues that is defined > by choosing the "min" and "max" residue numbers. When testing out > version 11.5.49 in order to take advantage of some of the great new > additions, I find that the line in my script with "max" is throwing > errors...specifically: > > select ligand; > nAtoms= {selected}.size; > rx = {selected}.resno.min; > ry = {selected}.resno.max; > > for (var i=rx;i<=ry;i=i+1) > ETC > > and here is the resulting error: > > 84 atoms selected > script ERROR: unrecognized atom property: 0x300092 > ----line 4 command 4 of file null: > ry = { selected } . resno . >> max << > > This happens both from my script and when entering the commands into > the console. BTW, I am using the applet in a web page.... > I would expect that I've created my own mistake, but this does work as > written in version 11.5.37. <http://11.5.37.>.... > > Thoughts? > > Thanks, > Tom > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >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: Alan H. <he...@il...> - 2008-07-26 16:28:02
|
Bob Hanson said: > This is fixed for 11.5.51 -- Nico, if you would please release that. > > CIF BETAij anisotropic support -- preliminary -- totally untested Thanks Bob, very welcome. I have installed it on ICSD http://icsd.ill.fr/ in which there are 6,657 structures (out of 100,000+) reporting Beta_ij, as recently as 2007, even though it is not officially defined in CIF :-) ______________________________________________ Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE <Alan.Hewat@NeutronOptics.com> +33.476.98.41.68 http://www.NeutronOptics.com/hewat ______________________________________________ |
From: Bob H. <ha...@st...> - 2008-07-28 13:08:17
|
whoa! Alan -- please VERIFY that it works before you endorse it. I ASSUMED this was ORTEP type 0. Nothing more. This needs checking! Also, it occurs to me that MAYBE the reason CIF format docs do not define these terms is that they are not known for sure -- that the betaij values might imply different definitions. Just something to check out. Bob Alan Hewat wrote: >Bob Hanson said: > > >>This is fixed for 11.5.51 -- Nico, if you would please release that. >> >>CIF BETAij anisotropic support -- preliminary -- totally untested >> >> > >Thanks Bob, very welcome. I have installed it on ICSD http://icsd.ill.fr/ >in which there are 6,657 structures (out of 100,000+) reporting Beta_ij, >as recently as 2007, even though it is not officially defined in CIF :-) >______________________________________________ >Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE ><Alan.Hewat@NeutronOptics.com> +33.476.98.41.68 > http://www.NeutronOptics.com/hewat >______________________________________________ > > >------------------------------------------------------------------------- >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: Alan H. <he...@il...> - 2008-07-28 14:28:31
|
Understood Bob. But as you know, a scientist finding some structure of interest in a database will ultimately want to go back to the original publication as the primary source. (Even that should be assumed to be sometimes wrong :-) I will check the Jmol drawings in ICSD as far as reasonable, but my experience is that if anyone finds errors they will let me know :-) So far, the orientation of your ellipsoids seems correct, but they may be larger than would be drawn by ORTEP. I have to check this more carefully. Already it is very useful. You can see immediately where the ellipsoids listed by ICSD are surely non-physical, or even non-positive definite (which is also flagged elsewhere, but there is nothing like a picture). Many thanks again. Alan. Bob Hanson said: > whoa! Alan -- please VERIFY that it works before you endorse it. I > ASSUMED this was ORTEP type 0. Nothing more. > > This needs checking! > > Also, it occurs to me that MAYBE the reason CIF format docs do not > define these terms is that they are not known for sure -- that the > betaij values might imply different definitions. Just something to check > out. > > Bob > > Alan Hewat wrote: > >>Bob Hanson said: >> >>>This is fixed for 11.5.51 -- Nico, if you would please release that. >>> >>>CIF BETAij anisotropic support -- preliminary -- totally untested >>> >>Thanks Bob, very welcome. I have installed it on ICSD http://icsd.ill.fr/ >>in which there are 6,657 structures (out of 100,000+) reporting Beta_ij, >>as recently as 2007, even though it is not officially defined in CIF :-) ______________________________________________ Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE <Alan.Hewat@NeutronOptics.com> +33.476.98.41.68 http://www.NeutronOptics.com/hewat ______________________________________________ |
From: Bob H. <ha...@st...> - 2008-07-26 01:32:33
|
they are available now. http://chemapps.stolaf.edu/jmol/docs/examples-11/ Thomas Stout wrote: > > Thanks for the quick fix Bob! I'll try it out as soon as I can get > the new files... > -Tom > > On Fri, Jul 25, 2008 at 4:40 PM, Bob Hanson <ha...@st... > <mailto:ha...@st...>> wrote: > > yes. ARGH! I know exactly what I did.... Thanks for spotting that. I > will have an update available later this evening. > > Bob > > Thomas Stout wrote: > > > > > Hi everyone -- > > > > I have a script that iterates over a range of residues that is > defined > > by choosing the "min" and "max" residue numbers. When testing out > > version 11.5.49 in order to take advantage of some of the great new > > additions, I find that the line in my script with "max" is throwing > > errors...specifically: > > > > select ligand; > > nAtoms= {selected}.size; > > rx = {selected}.resno.min; > > ry = {selected}.resno.max; > > > > for (var i=rx;i<=ry;i=i+1) > > ETC > > > > and here is the resulting error: > > > > 84 atoms selected > > script ERROR: unrecognized atom property: 0x300092 > > ----line 4 command 4 of file null: > > ry = { selected } . resno . >> max << > > > > This happens both from my script and when entering the commands into > > the console. BTW, I am using the applet in a web page.... > > I would expect that I've created my own mistake, but this does > work as > > written in version 11.5.37. <http://11.5.37.> <http://11.5.37.>.... > > > > Thoughts? > > > > Thanks, > > Tom > > > >------------------------------------------------------------------------ > > > >------------------------------------------------------------------------- > >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=/ > <http://moblin-contest.org/redirect.php?banner_id=100&url=/> > > > >------------------------------------------------------------------------ > > > >_______________________________________________ > >Jmol-users mailing list > >Jmo...@li... > <mailto: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 > > > > ------------------------------------------------------------------------- > 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=/ > <http://moblin-contest.org/redirect.php?banner_id=100&url=/> > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > <mailto:Jmo...@li...> > https://lists.sourceforge.net/lists/listinfo/jmol-users > > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >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: Thomas S. <tho...@gm...> - 2008-07-26 02:21:11
|
"max" is working just fine again..... Many thanks, again! -Tom On Fri, Jul 25, 2008 at 6:32 PM, Bob Hanson <ha...@st...> wrote: > they are available now. http://chemapps.stolaf.edu/jmol/docs/examples-11/ > > Thomas Stout wrote: > > > > > Thanks for the quick fix Bob! I'll try it out as soon as I can get > > the new files... > > -Tom > > > > On Fri, Jul 25, 2008 at 4:40 PM, Bob Hanson <ha...@st... > > <mailto:ha...@st...>> wrote: > > > > yes. ARGH! I know exactly what I did.... Thanks for spotting that. I > > will have an update available later this evening. > > > > Bob > > > > Thomas Stout wrote: > > > > > > > > Hi everyone -- > > > > > > I have a script that iterates over a range of residues that is > > defined > > > by choosing the "min" and "max" residue numbers. When testing out > > > version 11.5.49 in order to take advantage of some of the great new > > > additions, I find that the line in my script with "max" is throwing > > > errors...specifically: > > > > > > select ligand; > > > nAtoms= {selected}.size; > > > rx = {selected}.resno.min; > > > ry = {selected}.resno.max; > > > > > > for (var i=rx;i<=ry;i=i+1) > > > ETC > > > > > > and here is the resulting error: > > > > > > 84 atoms selected > > > script ERROR: unrecognized atom property: 0x300092 > > > ----line 4 command 4 of file null: > > > ry = { selected } . resno . >> max << > > > > > > This happens both from my script and when entering the commands > into > > > the console. BTW, I am using the applet in a web page.... > > > I would expect that I've created my own mistake, but this does > > work as > > > written in version 11.5.37. <http://11.5.37.> <http://11.5.37 > .>.... > > > > > > Thoughts? > > > > > > Thanks, > > > Tom > > > > > > >------------------------------------------------------------------------ > > > > > > >------------------------------------------------------------------------- > > >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=/ > > <http://moblin-contest.org/redirect.php?banner_id=100&url=/> > > > > > > >------------------------------------------------------------------------ > > > > > >_______________________________________________ > > >Jmol-users mailing list > > >Jmo...@li... > > <mailto: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 > > > > > > > > > ------------------------------------------------------------------------- > > 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=/ > > <http://moblin-contest.org/redirect.php?banner_id=100&url=/> > > _______________________________________________ > > Jmol-users mailing list > > Jmo...@li... > > <mailto:Jmo...@li...> > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > >------------------------------------------------------------------------ > > > >------------------------------------------------------------------------- > >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 > > > > ------------------------------------------------------------------------- > 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 > |