Hi Hyunmi, There are a few possible reasons, but it depends on the specific PDB file. Dotted lines are usually "pseudobonds," used to show where parts of chains are missing (such as a missing loop in a PDB structure due to poor density), metal complexation bonds, and distance measurements. You can hide it if you want by Ctrl-clicking to select it and then opening the Selection Inspector (by clicking the button on the lower right corner of the Chimera window) - in there, set "displayed" to "false". Or, you can open the PseudoBond Panel (under Tools... General Controls), click on the Name of that pseudobond group (different names are used for different situations), and then on the right side click close (delete) or hide. Or, you just could change how it looks by clicking "attributes..." and adjusting parameters in the resulting dialog. 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 Nov 9, 2007, at 9:06 AM, Hyunmi Sun wrote:
Dear Whom it may concern
Hello, I am currently using Chimera to access a pdb file. When I fetch the pdb file, one of the bonds between two ligands is illustrated as a dotted line in the wire representation. Why is this so?
Thanks for the help!
Sincerely, Hyunmi Sun