Re: [Jmol-users] MEP isosurface coloring
The charge range is beginning to sound familiar. I think I remember altering this years ago. The relative values of the color range and charge range are probably what will do the trick. Still have not found the command parameter but will be experimenting with it. Thanks. On Nov 11, 2008, at 4:31 AM, Angel Herraez wrote: > Frieda, I'd say that you can set a custom range for charges, then the > color range effectively used will be widened. > (I don't remember the syntax right now.) > > > - > 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 > Jmol-users@lists.sourceforge.net > 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MEP isosurface coloring
Altering the values in the color range parameter of the isosurface command makes the red and blue patches dimmer or brighter. The white areas increase to some extent because of the diminishing intensity of the red and blue areas, but the colors get very faint by the time there is any appreciable white area. Perhaps there is another parameter that I am not remembering. The documentation is still down; once it is back in business I will look for another parameter for charge range as opposed to color range. On Nov 11, 2008, at 4:31 AM, Angel Herraez wrote: > Frieda, I'd say that you can set a custom range for charges, then the > color range effectively used will be widened. > (I don't remember the syntax right now.) > > > - > 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 > Jmol-users@lists.sourceforge.net > 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MEP isosurface coloring
Frieda, I'd say that you can set a custom range for charges, then the color range effectively used will be widened. (I don't remember the syntax right now.) - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MEP isosurface coloring
Are you sure you're just not setting the range to your liking? On Mon, Nov 10, 2008 at 6:21 PM, Frieda Reichsman <[EMAIL PROTECTED]> wrote: > Any chance this would be a realistic feature request? For secondary school > teaching purposes we use the simpler, bwr color scheme that students are > already familiar with. It can be difficult for some students to have to > shift gears to another scheme. And showing areas that are hydrophobic is > critical, of course. > > > On Nov 10, 2008, at 7:09 PM, Robert Hanson wrote: > > no, I don't think so. > > On Mon, Nov 10, 2008 at 5:46 PM, Frieda Reichsman <[EMAIL PROTECTED]>wrote: > >> Hi Bob, >> >> Is there a mechanism, with the rwb or bwr colorshemes, for widening >> the white areas between the red and blue? Many published EP surfaces >> show large neutral regions; I have not figured out how to get Jmol to >> do this in rwb. These regions are green in the more extended color set. >> >> Thanks, >> Frieda >> >> >> - >> >> Frieda Reichsman, PhD >> Senior Research Scientist >> The Concord Consortium >> 25 Love Lane >> Concord, MA 01742 >> >> >> >> >> >> - >> 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 >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > 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 > Jmol-users@lists.sourceforge.net > 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 > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MEP isosurface coloring
Any chance this would be a realistic feature request? For secondary school teaching purposes we use the simpler, bwr color scheme that students are already familiar with. It can be difficult for some students to have to shift gears to another scheme. And showing areas that are hydrophobic is critical, of course. On Nov 10, 2008, at 7:09 PM, Robert Hanson wrote: no, I don't think so. On Mon, Nov 10, 2008 at 5:46 PM, Frieda Reichsman <[EMAIL PROTECTED]> wrote: Hi Bob, Is there a mechanism, with the rwb or bwr colorshemes, for widening the white areas between the red and blue? Many published EP surfaces show large neutral regions; I have not figured out how to get Jmol to do this in rwb. These regions are green in the more extended color set. Thanks, Frieda - Frieda Reichsman, PhD Senior Research Scientist The Concord Consortium 25 Love Lane Concord, MA 01742 - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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 Jmol-users@lists.sourceforge.net 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MEP isosurface coloring
no, I don't think so. On Mon, Nov 10, 2008 at 5:46 PM, Frieda Reichsman <[EMAIL PROTECTED]> wrote: > Hi Bob, > > Is there a mechanism, with the rwb or bwr colorshemes, for widening > the white areas between the red and blue? Many published EP surfaces > show large neutral regions; I have not figured out how to get Jmol to > do this in rwb. These regions are green in the more extended color set. > > Thanks, > Frieda > > > - > > Frieda Reichsman, PhD > Senior Research Scientist > The Concord Consortium > 25 Love Lane > Concord, MA 01742 > > > > > > - > 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 > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] MEP isosurface coloring
Hi Bob, Is there a mechanism, with the rwb or bwr colorshemes, for widening the white areas between the red and blue? Many published EP surfaces show large neutral regions; I have not figured out how to get Jmol to do this in rwb. These regions are green in the more extended color set. Thanks, Frieda - Frieda Reichsman, PhD Senior Research Scientist The Concord Consortium 25 Love Lane Concord, MA 01742 - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
