[Chimera-users] Pseudobonds in mmCIF

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 10 16:00:53 PST 2018


Hi Henry,
The simpler command is

~longbond

… but I am confused because in my tests of opening 1www.cif  (which has examples of missing segments pseudobonds) they are listed in the Pseudobond Panel as “missing segments” and these commands also work:

setattr p display false
setattr g display false

I’m testing with Chimera version 1.12.

Your description makes me think the offending connections may actually be bonds, not pseudobonds.  To say any more, we’d have to see the file… maybe something in there is wrong.  

If they are bonds, you can delete them with the ~bond command or in the Build Structure tool (in menu under Tools… Structure Editing) Adjust Bonds section.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#bond>

My only other idea is that they result from autochaining, which you can turn off with command:

setattr m autochain 0

(that’s a zero)

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 Jan 10, 2018, at 2:24 PM, Henry Nguyen <nguyen.henry.c at gmail.com> wrote:
> 
> Hi,
> 
> I am trying to disable all pseudobonds between gaps in my structure in an mmCIF file. I've tried: 
> 
> In the Pseudobond Panel, there is only one group (distance monitor) and it has 0 pseudobonds in the group.  Hiding that group doesn't change anything.
> 
> I also tried disabling them using setattrr ("setattr p display false"/ "setattr p display false") but neither didn't change anything.
> 
> If I select a psuedobond and examine it using the Selection Inspector, the Pseudobond tab is unselectable under Inspect. Only if I go to the Bond tab can I hide it.
> 
> I have to use mmCIF format as I have too many chains for a pdb.
> 
> Thanks,
> Henry






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