[Chimera-users] recovering saved pseudobonds; or convert pseudo to bond?

Elaine Meng meng at cgl.ucsf.edu
Fri Mar 25 08:31:01 PDT 2011

Hi Kelly,
It depends on what this cage model really is, in other words, what you mean by "manually created."   If you had used the command "hkcage" or "shape icosahedron" (or the Icosahedron Surface tool), it is a mesh surface, not pseudobonds, and can be made into bonds with the command "meshmol":


I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 25, 2011, at 5:49 AM, Kelly Dryden wrote:

> Hi,
> I have a series of saved selections that contain a combination of bonds and pseudobonds, but when I save the session and return to it, only the bonds are recalled.  All my attempts to convert the pseudobonds to "real" bonds have failed.  This is from a manually created cage model, without real atoms.  Is there anyway to either make all the connections into bonds, or to save the pseudobonds in the "named selections"? 
> Thanks,
> Kelly

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