Re: [Jmol-users] Atomistic model from source code, how to visualize it?

Dear Erkki, You may want to consider using the KiNG java applet instead of Jmol. KiNG is an implementation of MAGE, a program by David Richardson. MAGE is capable of handling many kinds of 3D data representations besides atoms, bonds, molecules. There are some Kinemages that demonstrate such uses

[Jmol-users] support for 3D mouse by 3Dconnexion in Jmol?

The molecular rover reminded me of something... The new 3D mouse by 3Dconnexion (http://www.3dconnexion.com/) seems like a good option for people doing visualization, but will Jmol be able to support it? Maybe someone could get a free one from the company in promise to make it work? There is a vi

Re: [Jmol-users] isosurface, mep, jvxl, and color

Beautiful. It works. Frieda On May 9, 2008, at 3:59 PM, Angel Herráez wrote: This seems to work: 1. create the isosurface with isosurface reversecolor colorscheme "rwb" sasurface 0.1 map mep 2. save it to jvxl 3. delete the isosurface isosurface delete 4. load it with isosurface colorscheme

Re: [Jmol-users] isosurface, mep, jvxl, and color

This seems to work: 1. create the isosurface with isosurface reversecolor colorscheme "rwb" sasurface 0.1 map mep 2. save it to jvxl 3. delete the isosurface isosurface delete 4. load it with isosurface colorscheme "bwr" # note that bwr is the opposite to rwb isosurface "Frieda-surface.jvxl"

Re: [Jmol-users] isosurface, mep, jvxl, and color

Hi Frieda Two quick ideas (untested): a) I'm not sure if yu can apply coloring togeher with isosurface loading, but guess you've tried that already b) There is an "isoSurface colorScheme" command that may be applied before loading the isosurface. HTH, --

[Jmol-users] Image Maps in Jmol wiki

This might be regarded as off topic, but I hope someone here reads PHP. I'm trying to get image maps to execute Jmol commands inside a MediaWiki using Nico's Jmol extension. Jmol windows are loading just fine but I need to pass the commands from the image maps. I contacted Tim Starling who w

[Jmol-users] MIssion:Immunity, an activity with Jmol

Hi All, [Apologies for double postings to those of you on both these lists.] Just thought you might want to check out an online activity in the immunology realm, that uses Jmol for 3D navigation. It is an exploration of cell surface MHC molecules, as if you are in a flying "Molecular Rover

[Jmol-users] isosurface, mep, jvxl, and color

Hi Bob, I'm working with a surface created as follows, from a MOL2 file: isosurface reversecolor colorscheme "rwb" sasurface 0.1 map mep On the page of examples here: http://chemapps.stolaf.edu/jmol/docs/examples-11/new0.htm example #82 shows that you can write a jvxl file of an mep surface an

[Jmol-users] AChE tutorial completed

Hi All, I have finally completed the AChE tutorial which can be viewed at http://www.messiah.edu/molscilab/jtat_080120/acetylcholinesterase/contents/contents.htm If you have not seen the other things that I developed at the Molecular Science Lab in the last 10 months go to the index of http:/