From a96d0378997f6afc20f526b0f3a6129d6d2f629f Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Thu, 19 Jul 2018 15:54:53 -0700
Subject: [PATCH] cartoon dna tweaks
---
.../structure/visual/nucleotide-block-mesh.ts | 2 +-
.../representation/structure/visual/util/polymer.ts | 2 +-
src/mol-view/stage.ts | 8 ++++++--
3 files changed, 8 insertions(+), 4 deletions(-)
diff --git a/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts b/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
index 1da058ee1..790a51a9e 100644
--- a/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
@@ -94,7 +94,7 @@ async function createNucleotideBlockMesh(ctx: RuntimeContext, unit: Unit, mesh?:
Vec3.normalize(v34, Vec3.sub(v34, p4, p3))
Vec3.normalize(vC, Vec3.cross(vC, v12, v34))
Mat4.targetTo(t, p1, p2, vC)
- Vec3.scaleAndAdd(center, p1, v12, height / 2)
+ Vec3.scaleAndAdd(center, p1, v12, height / 2 - 0.2)
Mat4.setTranslation(t, center)
builder.setId(SortedArray.findPredecessorIndex(elements, idx6))
builder.addBox(t, { width: width, height: depth, depth: height })
diff --git a/src/mol-geo/representation/structure/visual/util/polymer.ts b/src/mol-geo/representation/structure/visual/util/polymer.ts
index c6ed6ff0e..181869677 100644
--- a/src/mol-geo/representation/structure/visual/util/polymer.ts
+++ b/src/mol-geo/representation/structure/visual/util/polymer.ts
@@ -85,7 +85,7 @@ export function getResidueTypeAtomId(moleculeType: MoleculeType, atomType: 'trac
case MoleculeType.DNA:
switch (atomType) {
case 'trace': return 'C3\''
- case 'direction': return 'O4\''
+ case 'direction': return 'C1\''
}
break
}
diff --git a/src/mol-view/stage.ts b/src/mol-view/stage.ts
index fc98227bf..3f7e29c69 100644
--- a/src/mol-view/stage.ts
+++ b/src/mol-view/stage.ts
@@ -81,8 +81,12 @@ export class Stage {
// this.loadPdbid('4v5a') // ribosome
// this.loadPdbid('3j3q') // ...
// this.loadPdbid('2np2') // dna
- // this.loadPdbid('1d66') // dna
- this.loadPdbid('1bna') // B form dna
+ this.loadPdbid('1d66') // dna
+ // this.loadPdbid('9dna') // A form dna
+ // this.loadPdbid('1bna') // B form dna
+ // this.loadPdbid('199d') // C form dna
+ // this.loadPdbid('4lb6') // Z form dna
+ // this.loadPdbid('1egk') // 4-way dna-rna junction
// this.loadPdbid('1y26') // rna
// this.loadPdbid('1xv6') // rna, modified nucleotides
// this.loadPdbid('3bbm') // rna with linker
--
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