Hi Eric, Easy question first... I can think of three ways to turn off halfbond mode: - open the Model Panel (under Favorites), choose the models of interest in the left side, choose "attributes" on the right. In the model attributes panel, expand the "Component Bond Attributes" section, turn "halfbond mode" to "off" - select one or more bonds of interest, click the button on the lower right corner of the Chimera window that says what it selected (opens the Selection Inspector). In the Selection Inspector, go the bond section if you aren't there already, turn "halfbond mode" to "off" - use the command "bondcolor" (which also specifies a particular color for the bond) http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/bondcolor.html The Presets are pretty new, and currently there is no friendly way (without Python programming) to make your own presets. We plan to add this in the future. There is also no friendly way to transfer one molecule's attribute settings to another. However, there are some related things that may help: - the Preferences include a New Molecules section in which you can specify some display attributes of newly opened molecules. However, the options are not complete, i.e. not all attributes you might want are controllable there. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New% 20Molecules - if you have a series of commands that set the attributes, you can save them to a command file (or create a command file from scratch in a text editor). Opening the command file will execute all the commands. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ indexcommand.html#cmdfile - you can alias a long command or multiple semicolon-separated commands to a short string that is much easier to type. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html If you have specific suggestions or ideas, don't hesitate to share more information about your situation. We can factor them in to our plans. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jul 6, 2007, at 10:21 AM, Eric Ganz wrote:

Is there a way to create new presets for molecule views?

We want to apply the attributes of one molecule to subsequent molecules. Is there an easy way to do this?

Our second question is how to set half-bond mode off for our views.