-
Notifications
You must be signed in to change notification settings - Fork 1
Description
DK3Opa2-4DKDOpa2-OH
appears as:
DGulpx2-4DKDOpa
On the options page:
structure.pdb file looks to have the correct residue naming tho:
HEADER Produced by GMML (https://github.com/GLYCAM-Web/gmml2) version 1.5.1
ATOM 1 HO1 ROH 1 -3.767 9.090 -1.562 1.00 0.00 H
ATOM 2 O1 ROH 1 -4.172 9.583 -2.279 1.00 0.00 O
TER
ATOM 3 C2 4KO 2 -3.444 10.766 -2.524 1.00 0.00 C
ATOM 4 C1 4KO 2 -4.456 11.766 -3.336 1.00 0.00 C
ATOM 5 O1A 4KO 2 -5.174 12.525 -2.630 1.00 0.00 O
ATOM 6 O1B 4KO 2 -4.385 11.824 -4.588 1.00 0.00 O
ATOM 7 C3 4KO 2 -2.158 10.412 -3.314 1.00 0.00 C
ATOM 8 H3E 4KO 2 -2.393 9.775 -4.169 1.00 0.00 H
ATOM 9 H3A 4KO 2 -1.672 11.324 -3.672 1.00 0.00 H
ATOM 10 C4 4KO 2 -1.153 9.663 -2.420 1.00 0.00 C
ATOM 11 H4 4KO 2 -1.584 8.697 -2.153 1.00 0.00 H
ATOM 12 C5 4KO 2 -0.796 10.439 -1.115 1.00 0.00 C
ATOM 13 H5 4KO 2 -0.130 9.817 -0.514 1.00 0.00 H
ATOM 14 O5 4KO 2 -0.066 11.696 -1.414 1.00 0.00 O
ATOM 15 H5O 4KO 2 0.865 11.793 -1.042 1.00 0.00 H
ATOM 16 C6 4KO 2 -2.104 10.761 -0.362 1.00 0.00 C
ATOM 17 H6 4KO 2 -2.516 9.801 -0.051 1.00 0.00 H
ATOM 18 O6 4KO 2 -2.973 11.473 -1.264 1.00 0.00 O
ATOM 19 C7 4KO 2 -2.034 11.600 0.931 1.00 0.00 C
ATOM 20 H7 4KO 2 -1.863 12.639 0.646 1.00 0.00 H
ATOM 21 O7 4KO 2 -0.942 11.129 1.778 1.00 0.00 O
ATOM 22 H7O 4KO 2 -0.701 11.820 2.426 1.00 0.00 H
ATOM 23 C8 4KO 2 -3.348 11.512 1.761 1.00 0.00 C
ATOM 24 H81 4KO 2 -4.091 12.200 1.357 1.00 0.00 H
ATOM 25 H82 4KO 2 -3.746 10.497 1.721 1.00 0.00 H
ATOM 26 O8 4KO 2 -3.061 11.866 3.148 1.00 0.00 O
ATOM 27 H8O 4KO 2 -3.889 11.868 3.677 1.00 0.00 H
ATOM 28 O4 4KO 2 0.055 9.435 -3.190 1.00 0.00 O
TER
ATOM 29 O8 0KX 3 1.361 6.360 1.641 1.00 0.00 O
ATOM 30 H8O 0KX 3 2.158 6.679 2.039 1.00 0.00 H
ATOM 31 C8 0KX 3 1.123 7.074 0.438 1.00 0.00 C
ATOM 32 H8R 0KX 3 1.957 6.980 -0.243 1.00 0.00 H
ATOM 33 H8S 0KX 3 0.963 8.126 0.656 1.00 0.00 H
ATOM 34 C7 0KX 3 -0.132 6.479 -0.177 1.00 0.00 C
ATOM 35 H7 0KX 3 0.070 5.448 -0.440 1.00 0.00 H
ATOM 36 O7 0KX 3 -1.193 6.543 0.747 1.00 0.00 O
ATOM 37 H7O 0KX 3 -0.884 6.157 1.556 1.00 0.00 H
ATOM 38 C6 0KX 3 -0.574 7.236 -1.421 1.00 0.00 C
ATOM 39 H6 0KX 3 -0.905 8.223 -1.109 1.00 0.00 H
ATOM 40 O6 0KX 3 0.559 7.346 -2.247 1.00 0.00 O
ATOM 41 C2 0KX 3 0.413 8.092 -3.427 1.00 0.00 C
ATOM 42 C1 0KX 3 1.812 8.044 -4.140 1.00 0.00 C
ATOM 43 O1A 0KX 3 2.729 8.568 -3.528 1.00 0.00 O
ATOM 44 O1B 0KX 3 1.825 7.486 -5.249 1.00 0.00 O
ATOM 45 C3 0KX 3 -0.731 7.512 -4.277 1.00 0.00 C
ATOM 46 H3 0KX 3 -0.919 8.192 -5.101 1.00 0.00 H
ATOM 47 O3 0KX 3 -0.391 6.240 -4.771 1.00 0.00 O
ATOM 48 H3O 0KX 3 0.471 6.380 -5.188 1.00 0.00 H
ATOM 49 C4 0KX 3 -2.006 7.350 -3.448 1.00 0.00 C
ATOM 50 H4 0KX 3 -2.366 8.332 -3.172 1.00 0.00 H
ATOM 51 O4 0KX 3 -3.025 6.753 -4.204 1.00 0.00 O
ATOM 52 H4O 0KX 3 -2.686 5.922 -4.513 1.00 0.00 H
ATOM 53 C5 0KX 3 -1.720 6.554 -2.170 1.00 0.00 C
ATOM 54 H5 0KX 3 -2.603 6.548 -1.543 1.00 0.00 H
ATOM 55 O5 0KX 3 -1.433 5.210 -2.458 1.00 0.00 O
ATOM 56 H5O 0KX 3 -0.764 5.198 -3.136 1.00 0.00 H
TER
CONECT 2 3
CONECT 3 2
CONECT 28 41
CONECT 41 28
END
The messed up name is in the response.json:
"sequenceEvaluationOutput": {
"sequenceIsValid": true,
"sequenceVariants": {
"indexOrdered": "DK3Opa2-4DKDOpa2-OH",
"longestChainOrdered": "Currently unavailble in gmml. Request if needed!",
"userOrdered": "DK3Opa2-4DKDOpa2-OH",
"monospacedTextDiagram": null,
"indexOrderedLabeled": "DK3Op&Label=residue-3;a2-4&Label=link-1;DKDOp&Label=residue-2;a2-&Label=link-0;OH&Label=residue-1;",
"longestChainOrderedLabeled": null,
"userOrderedLabeled": null,
"monospacedTextDiagramLabeled": null,
"suuid": "d43b3f32-e1d6-5a49-8513-e9b153db8c03",
"smd5sum": null
},
"evaluationOptions": {
"validateOnly": false,
"evaluateForBuild": false,
"noBuild": false
},
"buildOptions": {
"solvationOptions": null,
"geometryOptions": {
"residues": null,
"linkages": {
"linkageRotamerInfo": {
"singleLinkageRotamerDataList": [
{
"indexOrderedLabel": "1",
"linkageLabel": null,
"linkageName": "DGulpx2-4DKDOpa",
"firstResidueNumber": "3",
"secondResidueNumber": "2",
"dihedralsWithOptions": [
"Phi"
],
The linkageName is probably coming from a reverse lookup with K:
{ "Gul", "K", "Saccharide"},
This is only an issue when communicating the linkage name to the user. The science is fine.