On Feb 17, 2009, at 1:15 PM, Jean-Paul Armache wrote:
hello, i have one question concerning color manipulation in chimera. every pdb file one opens gets a specific color (if set so). so, having a few of them open, one can distinguish between them color-wise. now, when one selects the files, it is possible to change the color via actions->color. this indeed changes all of the things selected, and if the whole pdb was selected, all the chains there. when one looks then into the model panel, the old colors are still there - untouched. this would be reasonable in the case when only parts of the pdb were selected and re-colored. however if one selects whole files and changes the colors - is it possible to have these colors changed also in the model panel? and is it possible to revert to the old color once changed through this action menu?
best regards, jean-paul armache
Hi Jean-Paul, It is because there is a coloring hierarchy: the Model Panel shows the model color, but you can also set atom colors, whichoverrule and hide the model color. As you found, Actions... Color and the "color" command set the atom colors (otherwise you would not be able to make different parts of the same model different colors). If you already colored the atoms of a model, you can "uncolor" some or all of them to reveal the model color using the command "~color". Another way is to choose "Actions... Color... from editor" and then click the "No Color" button in the Color Editor. (The Color Editor can be found in the menu under Tools... Utilities) You can change the model color with the command "modelcolor" or by clicking on the square color wells in the Model Panel to call up the Color Editor. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/coloring.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/hierarchy.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html