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

Kelly Dryden kdryden at virginia.edu
Fri Mar 25 09:10:22 PDT 2011

Hi Elaine,

No, the model was not made in Chimera.  It is a set of coordinates in a pdb file with "conect" parameters.  It's actually unclear to me why some are represented as bonds and others as pseudo, but the pseudobonds are classified as "missing segments" in the PseudoBond Panel.

I would still like to be able to recover pseudobonds that have been included in a named selection when returning to a saved session.  


On Fri, 25 Mar 2011 08:31:01 -0700
 Elaine Meng <meng at cgl.ucsf.edu> wrote:
>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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