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

[Eric Pettersen]

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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