Tether not shown to N-terminal OXT atom, pdb 3rum

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Minor stylistic thing for a rare modification...)

open 3rum
view /C:7

In the default cartoon representation, the C-terminal methyl ester appears as a detached carbon monoxide.

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3rum

Summary of feedback from opening 3rum fetched from pdb  
---  
notes | Fetching compressed mmCIF 3rum from
http://files.rcsb.org/download/3rum.cif  
Fetching CCD IPA from http://ligand-expo.rcsb.org/reports/I/IPA/IPA.cif  
Fetching CCD RST from http://ligand-expo.rcsb.org/reports/R/RST/RST.cif  
Fetching CCD CCS from http://ligand-expo.rcsb.org/reports/C/CCS/CCS.cif  
Fetching CCD HTY from http://ligand-expo.rcsb.org/reports/H/HTY/HTY.cif  
Fetching CCD MP4 from http://ligand-expo.rcsb.org/reports/M/MP4/MP4.cif  
Fetching CCD MDF from http://ligand-expo.rcsb.org/reports/M/MDF/MDF.cif  
  
3rum title:  
New strategy to analyze structures of glycopeptide antibiotic-target complexes
[more info...]  
  
Chain information for 3rum #1  
---  
Chain | Description  
A | Maltose-binding periplasmic protein  
B C | Ristocetin  
  
Non-standard residues in 3rum #1  
---  
BGC — beta-D-glucopyranose  
BXY — alpha-D-arabinofuranose  
GLC — alpha-D-glucopyranose  
HTY — (betaR)-beta-hydroxy-D-tyrosine  
IPA — isopropyl alcohol (2-propanol)  
MAN — alpha-D-mannopyranose  
MP4 — (2S)-amino(3,5-dihydroxy-4-methylphenyl)ethanoic acid  
RAM — alpha-L-rhamnopyranose  
RST — 3-amino-2,3,6-trideoxy-alpha-L-ribo-hexopyranose  
SO4 — sulfate ion  
  

> view :BXY

> show /C

> ~cartoon /C

> show cartoons




OpenGL version: 3.3.0 NVIDIA 455.32.00
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OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
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Cache Size: 20480 KB
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	Mem:            62G        3.6G         50G        124M        8.6G         58G
	Swap:          4.9G          0B        4.9G

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[Tom Goddard]

Elaine, Eric, in this ticket Tristan points out that the OXT and CH3 at the N-terminus of 3rum /C:7 is not showing a tether to the ribbon and that looks weird, looks like a carbon monoxide just sitting in space. I think I wasn't paying attention during those years of tether discussion group meetings so I don't understand the rules for what is supposed to be tethered. In the code there is a list of atom names that can show tethers:

static std::map<std::string, float> _tether_positions = {

Amino acid
{"N", -1/3.},
{"CA", 0.},
{"C", 1/3.},
Nucleotide
{"P", -2/6.},
{"O5'", -1/6.},
{"C5'", 0.},
{"C4'", 1/6.},
{"C3'", 2/6.},
{"O3'", 3/6.}

};

And then there is a list of atoms that don't show tether positions, although the point on the ribbon the project to is computed:

static std::map<std::string, float> _non_tether_positions = {

Amino acid
{"O", 1/3.},
{"OXT", 1/3.},
{"OT1", 1/3.},
{"OT2", 1/3.},
Nucleotide
{"OP1", -2/6.},
{"O1P", -2/6.},
{"OP2", -2/6.},
{"O2P", -2/6.},
{"OP3", -2/6.},
{"O3P", -2/6.},
{"O2'", -1/6.},
{"C2'", 2/6.},
{"O4'", 1/6.},
{"C1'", 1.5/6.},
{"O3'", 2/6.},

};

I see OXT is one of the atoms that won't show a tether.

Do you know why the code works this way? Why are these "non-tether" atoms such as OXT not allowed to show tethers?

The code defines certain atoms as ribbon backbone

{ "C", "CA", "N", "O", "OXT", "OT1", "OT2"};

and it also restricts the atoms that can show tethers to those that are "ribbon backbone". Why does the code allow tethers to C and N which seems useless and not to OXT? Is this just a mistake? I sense there is a logic to it that I am missing.

[Tom Goddard]

For reference Chimera 1.15 does connect the OXT to the ribbon -- look horrible, but it sensibly does want to connect it.

[Eric Pettersen]

In a normal amino acid, the OXT atom is only present at the C terminus of a chain. You do not want to show a floating tethered oxygen in that situation. This residue (MDF, a modified phenylalanine) is unusual in that it has a methyl group hanging off its OXT. Perhaps the "non-tether" rule has to be refined to also check that the atom has no more than one bond.

[Elaine Meng]

At least in olden days, the amino acid residues that were not the end of the chain would not have an OXT (T means terminus I think), but instead be capped by residue OME.

I see at ligand expo that OME is "obsoleted" so I don't know what policy is nowadays.  Seems weird to me to obsolete OME when the analogous endcap residue NME is not so tagged.

<http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=OME&operation=ccid>
<http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=NME&operation=ccid>

[Tom Goddard]

Fixed.

In the normal situation where the C-terminus has an OXT, the OXT is hidden when a ribbon is shown, so no tether is needed. In 3rum the C-terminus has an OXT-CH3 and the OXT is then not hidden by showing the ribbon. Although OXT is considered a ribbon backbone atom which would normally be hidden, I believe an ribbon backbone atom that is connected to another non-backbone atom is not hidden by the ribbon code. So I think OXT should get a tether when shown and it is just a mistake in the code. So I changed it to tether OXT when it is shown.