[chimerax-users] Pseudo bonds of missing structure in cartoon style

[Wout Oosterheert]

Hi Eric,

Thank you very much, I can confirm that my issue is resolved.

Best,
Wout

From: Eric Pettersen <pett at cgl.ucsf.edu>
Date: Wednesday, February 9, 2022 at 2:40 AM
To: Wout Oosterheert <wout.oosterheert at mpi-dortmund.mpg.de>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Pseudo bonds of missing structure in cartoon style

Hi Wout,
This bug is fixed and the fix will be in tonight's build.  Thanks for providing the structure offline.  It would have been impossible to figure out otherwise.

--Eric


On Feb 7, 2022, at 6:35 PM, Eric Pettersen <pett at cgl.ucsf.edu<mailto:pett at cgl.ucsf.edu>> wrote:

If they're all backbone atoms then I'm a little perplexed.  Is there any chance you could send me a session file?  Or a session file with everything but the problematic chain deleted, if you prefer...

--Eric

On Feb 5, 2022, at 3:20 AM, Wout Oosterheert <wout.oosterheert at mpi-dortmund.mpg.de<mailto:wout.oosterheert at mpi-dortmund.mpg.de>> wrote:

Dear Eric,

Thank you for the message. I am using version 1.3 (2021-12-08) for Mac. I have inspected the pdb and the endpoint atoms are all backbone atoms as far as I can see, so not sure what the problem is. There is by chance not a hidden maximum distance or angle for pseudobonds to appear?

Best,
Wout

From: Eric Pettersen <pett at cgl.ucsf.edu<mailto:pett at cgl.ucsf.edu>>
Reply-To: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>>
Date: Friday, February 4, 2022 at 8:46 PM
To: Wout Oosterheert <wout.oosterheert at mpi-dortmund.mpg.de<mailto:wout.oosterheert at mpi-dortmund.mpg.de>>
Cc: "chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>" <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>>
Subject: Re: [chimerax-users] Pseudo bonds of missing structure in cartoon style

Hi Wout,
What version of ChimeraX are you using?  Also, for the problematic pseudobond are either of its endpoint atoms not peptide backbone atoms?  If so, you will have to explicitly display the non-backbone atom in order for the pseudobond to show (display of backbone atoms is "implied" by the cartoon depiction).  Alternatively, you could delete the non-backbone atoms of the endpoint residue.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab




On Feb 4, 2022, at 9:19 AM, Wout Oosterheert via ChimeraX-users <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>> wrote:

Dear ChimeraX  team,

I’m making figures of a protein structure that has 4 residues missing in a flexible region. When I show the atoms as “style stick”, I can see a dashed pseudo bond between the two residues that connect the missing segment. However, when I “show cartoons” of the same structure, the dashed line disappears and the pseudo bond is no longer visible. Would you have any suggestions on what to change to make the missing structure appear as a dashed line when the model is shown in cartoon style?

Of interest, in a similar structure where 3 instead of 4 residues are missing, the dashed line is in fact shown when the model is shown in cartoon style. In addition, in regular Chimera the dashed line that represents the 4 missing residues remains visible in cartoon style.

Thank you for your time.

Best wishes,
Wout


Wout Oosterheert, PhD
Max Planck Institute of Molecular Physiology
Otto-Hahn-Str. 11
44227 Dortmund, Germany
Phone +49-(0)231-133-2357
Email: wout.oosterheert at mpi-dortmund.mpg.de<mailto:wout.oosterheert at mpi-dortmund.mpg.de>


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