Pseudo bonds of missing structure in cartoon style
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@mpi-dortmund.mpg.de<mailto:wout.oosterheert@mpi-dortmund.mpg.de>
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@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@mpi-dortmund.mpg.de <mailto:wout.oosterheert@mpi-dortmund.mpg.de>
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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@cgl.ucsf.edu> Reply-To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Date: Friday, February 4, 2022 at 8:46 PM To: Wout Oosterheert <wout.oosterheert@mpi-dortmund.mpg.de> Cc: "chimerax-users@cgl.ucsf.edu" <chimerax-users@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@cgl.ucsf.edu<mailto:chimerax-users@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@mpi-dortmund.mpg.de<mailto:wout.oosterheert@mpi-dortmund.mpg.de> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users
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@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@cgl.ucsf.edu> Reply-To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Date: Friday, February 4, 2022 at 8:46 PM To: Wout Oosterheert <wout.oosterheert@mpi-dortmund.mpg.de> Cc: "chimerax-users@cgl.ucsf.edu" <chimerax-users@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@cgl.ucsf.edu <mailto:chimerax-users@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@mpi-dortmund.mpg.de <mailto:wout.oosterheert@mpi-dortmund.mpg.de>
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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@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@mpi-dortmund.mpg.de <mailto:wout.oosterheert@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@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> Reply-To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Date: Friday, February 4, 2022 at 8:46 PM To: Wout Oosterheert <wout.oosterheert@mpi-dortmund.mpg.de <mailto:wout.oosterheert@mpi-dortmund.mpg.de>> Cc: "chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>" <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@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@cgl.ucsf.edu <mailto:chimerax-users@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@mpi-dortmund.mpg.de <mailto:wout.oosterheert@mpi-dortmund.mpg.de>
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Hi Eric, Thank you very much, I can confirm that my issue is resolved. Best, Wout From: Eric Pettersen <pett@cgl.ucsf.edu> Date: Wednesday, February 9, 2022 at 2:40 AM To: Wout Oosterheert <wout.oosterheert@mpi-dortmund.mpg.de> Cc: ChimeraX Users Help <chimerax-users@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@cgl.ucsf.edu<mailto:pett@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@mpi-dortmund.mpg.de<mailto:wout.oosterheert@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@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>> Reply-To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Date: Friday, February 4, 2022 at 8:46 PM To: Wout Oosterheert <wout.oosterheert@mpi-dortmund.mpg.de<mailto:wout.oosterheert@mpi-dortmund.mpg.de>> Cc: "chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>" <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@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@cgl.ucsf.edu<mailto:chimerax-users@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@mpi-dortmund.mpg.de<mailto:wout.oosterheert@mpi-dortmund.mpg.de> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users
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Eric Pettersen -
Wout Oosterheert