Re: nucleotide tube/slab or slab for modified nucleotides
A follow-up to the visualization of modified nucleotides as “slab”. The base of pseudouridine has the slab pointing in the wrong direction (probably due to the isomerization of the pyrimidine ring). This makes visualization of base pairs to PSU look wrong since the bases do not line up correctly (see attached image with PSU in purple in wrong position). Regards, Daniel From: Daniel Larsson via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Reply to: Daniel Larsson <daniel.larsson@icm.uu.se> Date: Wednesday, 13 May 2026 at 14:48 To: chimerax-users <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Re: nucleotide tube/slab or slab for modified nucleotides Hi Elaine, Thank you for the quick feedback. My problem was that I was using PDB files without the proper mmCIF headers. ChatGPT was helpful in explaining that non-standard residues can have a designated parental compound, which is defined in the mmCIF header: loop_ _chem_comp.id _chem_comp.mon_nstd_parent_comp_id 2MA A 2MG G Since I had several PDB files where I had done refinement, alignments, scaling and other things, I did not want to go through the trouble of converting them all to mmCIF. But fortunately, it seems ChimeraX only keeps one definition of monomer non-standard parent compounds, so it was sufficient for me to load one proper .mmCIF downloaded from the PDB so get the mapping correct. Short story, I just ran “open 7k00 fromDatabase pdb format mmcif” and after that all my modified nucleotides rendered correctly. Regards, Daniel From: Elaine Meng <meng@cgl.ucsf.edu> Reply to: chimerax-users <chimerax-users@cgl.ucsf.edu> Date: Tuesday, 12 May 2026 at 17:32 To: Daniel Larsson <daniel.larsson@icm.uu.se> Cc: Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] nucleotide tube/slab or slab for modified nucleotides Hi Daniel, In my test of a recent daily build, 2MA and 2MG in PDB 7k00 are shown as slabs. Maybe you need a newer version of ChimeraX? ChatGPT should always suggest getting a recent version -- then it might have a higher success rate. 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. [cid:image001.png@01DCF82D.773F82E0] There was a ticket previously to show slabs for more modified bases (#1211) but closed 18 months ago. Regards, 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 May 12, 2026, at 6:59 AM, Daniel Larsson via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Is it possible to show modified nucleotides as tube/slab or slab? Some common modified residues are recognized as nucleotides, such as PSU, but not e.g. 2MA or 2MG (present in e.g. PDB 7K00)? ChatGPT suggested to rename the residues or redefine the polymer type, but these tricks do not work.
Regards, Daniel
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This is a bug. I've created ticket #20483 for it and made Daniel the reporter. I'm going to discuss with our team if fixing this is worth holding up the immenint 1.12 release for. If not, it will be in a daily build soon. -- Greg On 6/9/2026 7:31 AM, Daniel Larsson via ChimeraX-users wrote:
Page Title
A follow-up to the visualization of modified nucleotides as “slab”. The base of pseudouridine has the slab pointing in the wrong direction (probably due to the isomerization of the pyrimidine ring). This makes visualization of base pairs to PSU look wrong since the bases do not line up correctly (see attached image with PSU in purple in wrong position).
Regards,
Daniel
*From: *Daniel Larsson via ChimeraX-users <chimerax-users@cgl.ucsf.edu> *Reply to: *Daniel Larsson <daniel.larsson@icm.uu.se> *Date: *Wednesday, 13 May 2026 at 14:48 *To: *chimerax-users <chimerax-users@cgl.ucsf.edu> *Subject: *[chimerax-users] Re: nucleotide tube/slab or slab for modified nucleotides
Hi Elaine,
Thank you for the quick feedback. My problem was that I was using PDB files without the proper mmCIF headers. ChatGPT was helpful in explaining that non-standard residues can have a designated parental compound, which is defined in the mmCIF header:
loop_ _chem_comp.id _chem_comp.mon_nstd_parent_comp_id 2MA A
2MG G
Since I had several PDB files where I had done refinement, alignments, scaling and other things, I did not want to go through the trouble of converting them all to mmCIF. But fortunately, it seems ChimeraX only keeps one definition of monomer non-standard parent compounds, so it was sufficient for me to load one proper .mmCIF downloaded from the PDB so get the mapping correct.
Short story, I just ran “open 7k00 fromDatabase pdb format mmcif” and after that all my modified nucleotides rendered correctly.
Regards,
Daniel
*From: *Elaine Meng <meng@cgl.ucsf.edu> *Reply to: *chimerax-users <chimerax-users@cgl.ucsf.edu> *Date: *Tuesday, 12 May 2026 at 17:32 *To: *Daniel Larsson <daniel.larsson@icm.uu.se> *Cc: *Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> *Subject: *Re: [chimerax-users] nucleotide tube/slab or slab for modified nucleotides
Hi Daniel, In my test of a recent daily build, 2MA and 2MG in PDB 7k00 are shown as slabs. Maybe you need a newer version of ChimeraX? ChatGPT should always suggest getting a recent version -- then it might have a higher success rate.
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.
There was a ticket previously to show slabs for more modified bases (#1211) but closed 18 months ago. Regards, 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 May 12, 2026, at 6:59 AM, Daniel Larsson via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Is it possible to show modified nucleotides as tube/slab or slab? Some common modified residues are recognized as nucleotides, such as PSU, but not e.g. 2MA or 2MG (present in e.g. PDB 7K00)? ChatGPT suggested to rename the residues or redefine the polymer type, but these tricks do not work.
Regards, Daniel
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
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.
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This has been fixed and the fix will show up in the imminent ChimeraX 1.12 and the next daily build. -- Greg On 6/10/26 12:12, Greg Couch via ChimeraX-users wrote:
This is a bug. I've created ticket #20483 for it and made Daniel the reporter. I'm going to discuss with our team if fixing this is worth holding up the immenint 1.12 release for. If not, it will be in a daily build soon.
-- Greg
On 6/9/2026 7:31 AM, Daniel Larsson via ChimeraX-users wrote:
Page Title
A follow-up to the visualization of modified nucleotides as “slab”. The base of pseudouridine has the slab pointing in the wrong direction (probably due to the isomerization of the pyrimidine ring). This makes visualization of base pairs to PSU look wrong since the bases do not line up correctly (see attached image with PSU in purple in wrong position).
Regards,
Daniel
*From: *Daniel Larsson via ChimeraX-users <chimerax-users@cgl.ucsf.edu> *Reply to: *Daniel Larsson <daniel.larsson@icm.uu.se> *Date: *Wednesday, 13 May 2026 at 14:48 *To: *chimerax-users <chimerax-users@cgl.ucsf.edu> *Subject: *[chimerax-users] Re: nucleotide tube/slab or slab for modified nucleotides
Hi Elaine,
Thank you for the quick feedback. My problem was that I was using PDB files without the proper mmCIF headers. ChatGPT was helpful in explaining that non-standard residues can have a designated parental compound, which is defined in the mmCIF header:
loop_ _chem_comp.id _chem_comp.mon_nstd_parent_comp_id 2MA A
2MG G
Since I had several PDB files where I had done refinement, alignments, scaling and other things, I did not want to go through the trouble of converting them all to mmCIF. But fortunately, it seems ChimeraX only keeps one definition of monomer non-standard parent compounds, so it was sufficient for me to load one proper .mmCIF downloaded from the PDB so get the mapping correct.
Short story, I just ran “open 7k00 fromDatabase pdb format mmcif” and after that all my modified nucleotides rendered correctly.
Regards,
Daniel
*From: *Elaine Meng <meng@cgl.ucsf.edu> *Reply to: *chimerax-users <chimerax-users@cgl.ucsf.edu> *Date: *Tuesday, 12 May 2026 at 17:32 *To: *Daniel Larsson <daniel.larsson@icm.uu.se> *Cc: *Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> *Subject: *Re: [chimerax-users] nucleotide tube/slab or slab for modified nucleotides
Hi Daniel, In my test of a recent daily build, 2MA and 2MG in PDB 7k00 are shown as slabs. Maybe you need a newer version of ChimeraX? ChatGPT should always suggest getting a recent version -- then it might have a higher success rate.
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.
There was a ticket previously to show slabs for more modified bases (#1211) but closed 18 months ago. Regards, 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 May 12, 2026, at 6:59 AM, Daniel Larsson via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Is it possible to show modified nucleotides as tube/slab or slab? Some common modified residues are recognized as nucleotides, such as PSU, but not e.g. 2MA or 2MG (present in e.g. PDB 7K00)? ChatGPT suggested to rename the residues or redefine the polymer type, but these tricks do not work.
Regards, Daniel
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
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/
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participants (2)
-
Daniel Larsson -
Greg Couch