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

Eric Pettersen pett at cgl.ucsf.edu
Mon Mar 28 17:24:44 PDT 2011

Starting with tomorrow's 1.6 daily builds, Chimera will remember the  
selection status of pseudobonds.


On Mar 25, 2011, at 10:27 AM, Eric Pettersen wrote:

> Hi Kelly,
> 	You are right that sessions don't save the pseudobond part of
> selections.  I will do something about that next week.  In the interim
> I have an alternative that you'll probably like better anyway.
> "Missing segments" are where Chimera has judged that part of the
> structure is missing because the bond between two atoms is too long
> and there is a gap in the sequence numbering between those atoms.  It
> shows a pseudobond in that case, but the regular bond is still there,
> just never displayed.  Here's how to hide the pseudobonds and show the
> hidden actual bonds:
> 1) Go to Tools->General Controls->Pseudobond Panel and hide "missing
> segments"
> 2) In the command line type "sel #" to select everything in your
> structure
> 3) Type "setattr b display 2 sel" to change all bonds display mode to
> 2 ("smart").  The hidden bonds were in display mode 0 ("never").
> --Eric
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
> On Mar 25, 2011, at 9:10 AM, Kelly Dryden wrote:
>> 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.
>> Thanks,
>> Kelly
>> 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":
>>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html>
>>> 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
>>> 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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