Hi Enrico, As Elaine pointed out, you can't form a covalent bond between two models (since that's the definition of "model" in Chimera). Forming a pseudobond as Elaine outlines is one possibility. The other alternative is to combine the two models into one by using the "combine" command or the "copy/combine" button of the Model Panel. Once you have a single model you can then use the "bond" command to form a bond between the atoms. However, I recommend Elaine's approach unless there's a specific reason you need a single model (such as writing out a PDB file without MODEL records). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On May 18, 2009, at 9:38 AM, Elaine Meng wrote:
Dear Enrico, Chimera doesn't allow adding a bond between two different models (structures opened from two different files), but if you mainly want the appearance of a bond, you can create a "pseudobond" connecting the atoms.
Pseudobonds are just lines drawn between any pair of atoms. You can control their style, thickness, color, and labels. To make pseudobonds, create a text file where each line gives the two atoms to be connected, and the desired color and optional label. In your case the file might be only one line. Then use the Pseudobond Reader tool to open the text file and create the pseudobond(s). Here is the description of that tool and the file format: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.h...
For further changes such as line style and color, open Pseudobond Panel (under Tools... General Controls), and in that dialog choose your pseudobonds on the left side and click the "attributes..." button on the right. That will bring up another window with options to adjust the display. Such changes could also be done with the "setattr" command, but it is trickier. You may want to make your new pseudobond look the same as other metal complex pseudobonds (default medium purple, linewidth 2.5, dashed) <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Molec...
Currently there is no command to add pseudobonds. You could make the pseudobond ahead of time and undisplay it, then show it later within a script, using the "setattr" command:
setattr p display false ions z<4 setattr p display true ions z<4
where the "ions z<4" part limits the effect to only pseudobonds around ions. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. 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 May 18, 2009, at 8:22 AM, Enrico Morelli wrote:
Dear all, We would like to know if is it possible, when we have two molecules docked together, to form a coordination bond between a metal ion present in one of the two molecules and a donor atom of the other molecule, in such way forming a covalent bond between the two proteins. Thanks
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