Hi Ryan, It is because there is an upper limit to how many pixels wide a "wire" can be drawn. It varies from machine to machine. When there is a high final dpi and/or supersampling, that means the initial drawing needs to be quite fat to achieve the desired final appearance. There can be a mismatch between the upper limit for the "dot" fatness (the atoms) and "wire" fatness. You can probably see it without saving an image by simply setting a ridiculously high linewidth, for example with the command: linewidth 20 and zooming in so you can see the atoms and bonds. Since the linewidth is in pixels and not in units of length, it is not constant relative to the scale of the molecule. There is no way I know of to avoid the mismatch other than to reduce the amount of supersampling, the dpi, and/or the linewidth. There is an attempt to estimate what linewidth is possible in saved images for your requested dpi and supersampling level - the File... Save Image dialog it will contain a message something like "effective maximum line width is 3.3333" You may also want to try showing sticks instead of the wire representation. Best, 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 On Sep 9, 2008, at 8:24 AM, Ryan wrote:

Hi, I am trying to save higher resolution images that contain some residues with a wire width of 2. I have noticed that when i increase the dpi of the images, the saved images look different than what is displayed in the viewer -- nodes appear at each atom of the residues that are displayed as wires. As i increase the dpi of the saved images, the nodes become increasingly exaggerated (of a thicker radius than the wire bonds). Is this what should be happening? If so, is there a way to have both the atoms and bonds save with the same radius? Thanks a lot,