morph command ignores ions in metalloproteins?
Hello, I am trying to make a morph between PDB entries 9SKS and 9SKT. The protein does what I want, but I can't find out how to include the active site :ZN in the interpolation. This ion is consistently numbered between both structures, and I give model numbers to the morph command, which should select the entire models including their ions. Nothing about this in the documentation. What am I missing? If interpolating ions with morph is impossible to do for some reason, then it would be helpful to list it in the "limitations" section<https://www.cgl.ucsf.edu/chimerax/docs/user/commands/morph.html#limitations> of the command's documentation. Thank you in advance, Guillaume --- Guillaume Gaullier, PhD Researcher, Blikstad group Molecular Biomimetics / Microbial Chemistry Department of Chemistry - Ångström Uppsala University Regementsvägen 10 752 37 Uppsala Sweden När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
Hi Guillame, It's covered in the "atoms in common" section of the morph documentation. Namely, you need to use "same true": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing> The zinc is in the morph when I have these structures open as #1 and #2 and use command morph #1,2 same true I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 30, 2026, at 2:23 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I am trying to make a morph between PDB entries 9SKS and 9SKT. The protein does what I want, but I can't find out how to include the active site :ZN in the interpolation. This ion is consistently numbered between both structures, and I give model numbers to the morph command, which should select the entire models including their ions. Nothing about this in the documentation. What am I missing?
If interpolating ions with morph is impossible to do for some reason, then it would be helpful to list it in the "limitations" section of the command's documentation.
Thank you in advance,
Guillaume
--- Guillaume Gaullier, PhD Researcher, Blikstad group Molecular Biomimetics / Microbial Chemistry Department of Chemistry - Ångström Uppsala University Regementsvägen 10 752 37 Uppsala Sweden
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy_________________________... ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Once more I skimmed the documentation too fast... thank you! 😊 ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, September 30, 2026 5:37:55 PM To: Guillaume Gaullier Cc: ChimeraX Users Help Subject: Re: [chimerax-users] morph command ignores ions in metalloproteins? Hi Guillame, It's covered in the "atoms in common" section of the morph documentation. Namely, you need to use "same true": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing> The zinc is in the morph when I have these structures open as #1 and #2 and use command morph #1,2 same true I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 30, 2026, at 2:23 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I am trying to make a morph between PDB entries 9SKS and 9SKT. The protein does what I want, but I can't find out how to include the active site :ZN in the interpolation. This ion is consistently numbered between both structures, and I give model numbers to the morph command, which should select the entire models including their ions. Nothing about this in the documentation. What am I missing?
If interpolating ions with morph is impossible to do for some reason, then it would be helpful to list it in the "limitations" section of the command's documentation.
Thank you in advance,
Guillaume
--- Guillaume Gaullier, PhD Researcher, Blikstad group Molecular Biomimetics / Microbial Chemistry Department of Chemistry - Ångström Uppsala University Regementsvägen 10 752 37 Uppsala Sweden
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy_________________________... ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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And is there a way to display the ion coordination pseudo-bonds all the way through the interpolation? Now they are only displayed (even only seem to exist?) on the first frame, and the coordset documentation doesn't mention this (I read more carefully this time...). If not I will simply hide the pseudo-bonds. Thank you, Guillaume ________________________________ From: Guillaume Gaullier Sent: Thursday, October 1, 2026 9:57:42 AM To: ChimeraX Users Help Subject: Re: [chimerax-users] morph command ignores ions in metalloproteins? Once more I skimmed the documentation too fast... thank you! 😊 ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, September 30, 2026 5:37:55 PM To: Guillaume Gaullier Cc: ChimeraX Users Help Subject: Re: [chimerax-users] morph command ignores ions in metalloproteins? Hi Guillame, It's covered in the "atoms in common" section of the morph documentation. Namely, you need to use "same true": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing> The zinc is in the morph when I have these structures open as #1 and #2 and use command morph #1,2 same true I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 30, 2026, at 2:23 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I am trying to make a morph between PDB entries 9SKS and 9SKT. The protein does what I want, but I can't find out how to include the active site :ZN in the interpolation. This ion is consistently numbered between both structures, and I give model numbers to the morph command, which should select the entire models including their ions. Nothing about this in the documentation. What am I missing?
If interpolating ions with morph is impossible to do for some reason, then it would be helpful to list it in the "limitations" section of the command's documentation.
Thank you in advance,
Guillaume
--- Guillaume Gaullier, PhD Researcher, Blikstad group Molecular Biomimetics / Microbial Chemistry Department of Chemistry - Ångström Uppsala University Regementsvägen 10 752 37 Uppsala Sweden
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy_________________________... ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe.
Hi Guillaume, Some kinds of pseudobonds are tracked for each coordinate set (e.g. hydrogen bonds, metal-coordination bonds) and some are not (e.g. missing structure). Your only real option here is to hide the coordination bonds. I am working on porting the Metal Geometry tool from Chimera, and that will have an option to add coordination bonds throughout a trajectory/interpolation, but it’s still probably weeks before the tool will be finished. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Oct 1, 2026, at 2:46 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
And is there a way to display the ion coordination pseudo-bonds all the way through the interpolation? Now they are only displayed (even only seem to exist?) on the first frame, and the coordset documentation doesn't mention this (I read more carefully this time...). If not I will simply hide the pseudo-bonds.
Thank you,
Guillaume From: Guillaume Gaullier Sent: Thursday, October 1, 2026 9:57:42 AM To: ChimeraX Users Help Subject: Re: [chimerax-users] morph command ignores ions in metalloproteins?
Once more I skimmed the documentation too fast... thank you! 😊 From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, September 30, 2026 5:37:55 PM To: Guillaume Gaullier Cc: ChimeraX Users Help Subject: Re: [chimerax-users] morph command ignores ions in metalloproteins?
Hi Guillame, It's covered in the "atoms in common" section of the morph documentation. Namely, you need to use "same true":
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing>
The zinc is in the morph when I have these structures open as #1 and #2 and use command
morph #1,2 same true
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 30, 2026, at 2:23 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I am trying to make a morph between PDB entries 9SKS and 9SKT. The protein does what I want, but I can't find out how to include the active site :ZN in the interpolation. This ion is consistently numbered between both structures, and I give model numbers to the morph command, which should select the entire models including their ions. Nothing about this in the documentation. What am I missing?
If interpolating ions with morph is impossible to do for some reason, then it would be helpful to list it in the "limitations" section of the command's documentation.
Thank you in advance,
Guillaume
--- Guillaume Gaullier, PhD Researcher, Blikstad group Molecular Biomimetics / Microbial Chemistry Department of Chemistry - Ångström Uppsala University Regementsvägen 10 752 37 Uppsala Sweden
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy_________________________... ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Thank you Eric. Yes I figured the easiest for now is to hide these bonds. ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Thursday, October 1, 2026 10:31:26 PM To: Guillaume Gaullier Cc: ChimeraX Users Help Subject: Re: [chimerax-users] morph command ignores ions in metalloproteins? Hi Guillaume, Some kinds of pseudobonds are tracked for each coordinate set (e.g. hydrogen bonds, metal-coordination bonds) and some are not (e.g. missing structure). Your only real option here is to hide the coordination bonds. I am working on porting the Metal Geometry tool from Chimera, and that will have an option to add coordination bonds throughout a trajectory/interpolation, but it’s still probably weeks before the tool will be finished. --Eric Eric Pettersen UCSF Computer Graphics Lab On Oct 1, 2026, at 2:46 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: And is there a way to display the ion coordination pseudo-bonds all the way through the interpolation? Now they are only displayed (even only seem to exist?) on the first frame, and the coordset documentation doesn't mention this (I read more carefully this time...). If not I will simply hide the pseudo-bonds. Thank you, Guillaume ________________________________ From: Guillaume Gaullier Sent: Thursday, October 1, 2026 9:57:42 AM To: ChimeraX Users Help Subject: Re: [chimerax-users] morph command ignores ions in metalloproteins? Once more I skimmed the documentation too fast... thank you! 😊 ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, September 30, 2026 5:37:55 PM To: Guillaume Gaullier Cc: ChimeraX Users Help Subject: Re: [chimerax-users] morph command ignores ions in metalloproteins? Hi Guillame, It's covered in the "atoms in common" section of the morph documentation. Namely, you need to use "same true": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing> The zinc is in the morph when I have these structures open as #1 and #2 and use command morph #1,2 same true I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 30, 2026, at 2:23 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I am trying to make a morph between PDB entries 9SKS and 9SKT. The protein does what I want, but I can't find out how to include the active site :ZN in the interpolation. This ion is consistently numbered between both structures, and I give model numbers to the morph command, which should select the entire models including their ions. Nothing about this in the documentation. What am I missing?
If interpolating ions with morph is impossible to do for some reason, then it would be helpful to list it in the "limitations" section of the command's documentation.
Thank you in advance,
Guillaume
--- Guillaume Gaullier, PhD Researcher, Blikstad group Molecular Biomimetics / Microbial Chemistry Department of Chemistry - Ångström Uppsala University Regementsvägen 10 752 37 Uppsala Sweden
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy_________________________... ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe.
participants (3)
-
Elaine Meng -
Eric Pettersen -
Guillaume Gaullier