Carbohydrate Builder-2 issues

[dnago4]

Tool:
Carbohydrate Builder

Bug Description:
On structure viewer for "DGalp[3S]b1-4[LFucpa1-3]DGlcpNAc[6S]b1-OH"

1. "SO3" show floating positions close to Galp and GlcpNAc at appropriate positions, but NO linkage to C3O- or C6O-
2. downloaded PDB structure displays different problems: a) Galp not bonded to GlcpNAc, instead Galp shown with C1-OH; b) Fucp not bonded to GlcpNAc, instead Fucp shown with C1-OH. In both cases GlcpNAc also appears with C4,3 OH intact.

To Reproduce:
Build structure:

1. Done, then taken to viewer--see 'floating' SO3s
2. Download PDB--view in structure viewer to see unlinked structures

Expected behavior
Bonds expected to present as one molecule rather than independent entities

Screenshots
If applicable, add screenshots to help explain your problem.

Device & OS Details
Browser: Chrome 141.0.7390.123 (Official Build) (64-bit)
OS: Windows 10, 22H2

Bug#1

Bug#2

Thanks for viewing this report!

[gitoliver]

Thanks for reporting!

Bug 1 is a known visualization issue #192. The TER cards have to be there for tleap, but they cause breaks in Mol* even though we add CONECT cards. Probably we need to adjust a setting in Mol* for this to work. @danwentworthart can you find out what we need to do? It does not help with user confidence in the results.

Bug 2 looks serious, but I can't reproduce it. When I download and check structure.pdb or min-gas.pdb they do not contain hydrogens on the substituted positions.
"Download PDB--view in structure viewer to see unlinked structures" What is structure viewer? Are you re-uploading to Mol* somewhere? I wonder if whatever viewer you are using is adding the hydrogens automatically?

Here are my results from using actual (glycam.org) today:
DGalp[3S]b1-4[LFucpa1-3]DGlcpNAc[6S]b1-OH.zip

[danwentworthart]

Yes, I can look into this.

[dnago4]

Thank you for your reply! I may not have been clear on item #2 because, because I asked for Hs to show in the most recent ChimeraX. It was only the 'min-gas.pdb' file that I downloaded. There are differences in the way 'min-gas.pdb' and 'structure.pdb' (that you provided) display. While the Hs do not usually display (I did that just to see how the structure was chemically defined in the PDB), 'min-gas.pdb' appears with Hs in all appropriate atom positions. However, Cs #1 of both GalNAc and Fuc show incomplete bonding, as well as corresponding Os in GlcNAc, confirming that what was displayed was intended but not fully completed graphically in ChimeraX. Perhaps this seems to be an 'atypical or incomplete' specification in the 'min-gas.pdb, and an explicit completion of bonding is needed? At least for ChimeraX processing. I dont know as I am not proficient in parsing the PDB file. This may be something I need to raise for that package. What is interesting, and gets you in the clear, is that Open Babel has no issue and converts 'min-gas.pdb' to SDF that displays well. So indeed, ChimeraX might need tweaking. Hope this helps. Dan

…

On Mon, Oct 27, 2025 at 5:23 AM Oliver ***@***.***> wrote: *gitoliver* left a comment (GLYCAM-Web/website#282) <#282 (comment)> Thanks for reporting! Bug 1 is a known visualization issue #192 <#192>. The TER cards have to be there for tleap, but they cause breaks in Mol* even though we add CONECT cards. Probably we need to adjust a setting in Mol* for this to work. @danwentworthart <https://github.com/danwentworthart> can you find out what we need to do? It does not help with user confidence in the results. Bug 2 looks serious, but I can't reproduce it. When I download and check structure.pdb or min-gas.pdb they do not contain hydrogens on the substituted positions. "Download PDB--view in structure viewer to see unlinked structures" What is structure viewer? Are you re-uploading to Mol* somewhere? I wonder if whatever viewer you are using is adding the hydrogens automatically? Here are my results from using actual (glycam.org) today: DGalp[3S]b1-4[LFucpa1-3]DGlcpNAc[6S]b1-OH.zip <https://github.com/user-attachments/files/23164065/DGalp.3S.b1-4.LFucpa1-3.DGlcpNAc.6S.b1-OH.zip> — Reply to this email directly, view it on GitHub <#282 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASIFPPONHBSTN5MT3L335AT3ZX6E3AVCNFSM6AAAAACKIFEKFOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTINJRGAYTIMJSGI> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[gitoliver]

Hi Dan,

I've experienced similar things in the original UCSF Chimera with GLYCAM residues. I had to select the residues and "add reasonable bonds" between them. For now I don't see this as a bug on our end. In future we could produce more ChimeraX friendly formatted pdb files if that helps people. We have a grant application in that if funded will look for these types of improvements that help broaden our usefulness.

[dnago4]

Hi Oliver Hope you do get funded because this utility is essential for glycobiologists! I had considered this a bug until trying your structure.pdf file, though I have had similar zip downloads and don't remember getting any to work. Now I know it is a ChimeraX thing, and have submitted a ticket for it. In the future I know the workaround. Just like everything else an option B is always necessary. But I don't think there is one for GLYCAM. Appreciate your work! Best regards Dan

…

On Tue, Oct 28, 2025 at 5:52 AM Oliver ***@***.***> wrote: *gitoliver* left a comment (GLYCAM-Web/website#282) <#282 (comment)> Hi Dan, I've experienced similar things in the original UCSF Chimera with GLYCAM residues. I had to select the residues and "add reasonable bonds" between them. For now I don't see this as a bug on our end. In future we could produce more ChimeraX friendly formatted pdb files if that helps people. We have a grant application in that if funded will look for these types of improvements that help broaden our usefulness. — Reply to this email directly, view it on GitHub <#282 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASIFPPPVKUYVAXJ4JEHOSLL3Z5RITAVCNFSM6AAAAACKIFEKFOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTINJWGMZDONJSHA> . You are receiving this because you authored the thread.Message ID: ***@***.***>