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Mechanism for activation of OR6A/B/P/Y receptors by aldehydes. #390

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Mechanism for activation of OR6A/B/P/Y receptors by aldehydes. #390

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25 changes: 23 additions & 2 deletions src/ic_activate_or.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -134,9 +134,11 @@ int main(int argc, char** argv)
AminoAcid *aa6x53 = p.get_residue_bw("6.53");
AminoAcid *aa6x54 = p.get_residue_bw("6.54");
AminoAcid *aa6x55 = p.get_residue_bw("6.55");
AminoAcid *aa6x57 = p.get_residue_bw("6.57");
AminoAcid *aa6x58 = p.get_residue_bw("6.58");
AminoAcid *aa6x59 = p.get_residue_bw("6.59");
AminoAcid *aa7x31 = p.get_residue_bw("7.31");
AminoAcid *aa7x34 = p.get_residue_bw("7.34");
AminoAcid *aa7x37 = p.get_residue_bw("7.37");
AminoAcid *aa7x41 = p.get_residue_bw("7.41");
AminoAcid *aa7x42 = p.get_residue_bw("7.42");
Expand All @@ -162,12 +164,14 @@ int main(int argc, char** argv)
int n4x64 = aa4x64->get_residue_no();
int n45x51 = aa45x51->get_residue_no();
int n5x33 = aa5x33->get_residue_no();
int n5x39 = aa5x39->get_residue_no();
int n5x50 = aa5x50->get_residue_no();
int n5x68 = aa5x68->get_residue_no();
int n56x50 = aa56x50->get_residue_no();
int n6x28 = aa6x28->get_residue_no();
int n6x48 = aa6x48->get_residue_no();
int n6x55 = aa6x55->get_residue_no();
int n6x57 = aa6x57->get_residue_no();
int n6x58 = aa6x58->get_residue_no();
int n6x59 = aa6x59->get_residue_no();
int n7x31 = aa7x31->get_residue_no();
Expand All @@ -180,15 +184,19 @@ int main(int argc, char** argv)
char l3x40 = aa3x40->get_letter();
char l4x52 = aa4x52->get_letter();
char l4x56 = aa4x56->get_letter();
char l4x60 = aa4x60->get_letter();
char l45x51 = aa45x51->get_letter();
char l45x52 = aa45x52->get_letter();
char l45x53 = aa45x53->get_letter();
char l5x39 = aa5x39->get_letter();
char l5x50 = aa5x50->get_letter();
char l5x58 = aa5x58->get_letter();
char l6x48 = aa6x48->get_letter();
char l6x55 = aa6x55->get_letter();
char l6x57 = aa6x57->get_letter();
char l6x58 = aa6x58->get_letter();
char l6x59 = aa6x59->get_letter();
char l7x34 = aa7x34->get_letter();
char l7x41 = aa7x41->get_letter();
char l7x53 = aa7x53->get_letter();

Expand Down Expand Up @@ -218,6 +226,7 @@ int main(int argc, char** argv)
Bond* b;
bool bcr;
bool stiff6x55 = false;
bool or6abpy = false;

LocatedVector axis1, axis2, axis3, axis4, axis5, axis6, axis7;
float theta;
Expand All @@ -238,6 +247,11 @@ int main(int argc, char** argv)
// Receptor-specific fixes.
////////////////////////////////////////////////////////////////////////////////

if (l4x60 == 'K' && l5x39 == 'D' && (l6x57 == 'R' || l6x57 == 'K') && (l7x34 == 'N' || l7x34 == 'Q'))
{
or6abpy = true;
}

if (l6x55 == 'D' || l6x55 == 'E' || l6x55 == 'R' || l6x55 == 'K') // OR1G1 is an example.
{
pt_tmp = aa6x55->get_CA_location().subtract(aa45x51->get_reach_atom()->get_location());
Expand Down Expand Up @@ -348,7 +362,7 @@ int main(int argc, char** argv)
float r = aa6x55->get_atom("OH")->distance_to(aa45x51->get_nearest_atom(aa6x55->get_atom_location("HH")));
aa6x55->conform_atom_to_location(aa6x55->get_reach_atom()->name, Point(0,10000,0));

if (r <= 3)
if (false) // r <= 3)
{
if (l6x48 == 'Y' && (l3x40 == 'S' || l3x40 == 'T' && l3x40 == 'N' || l3x40 == 'Q' || l3x40 == 'E' || l3x40 == 'D'))
{
Expand Down Expand Up @@ -691,7 +705,7 @@ int main(int argc, char** argv)
// Compute the angle to rotate about 6.48 and perform the rotation. Measure how far 56.50 moved; call it TMR6c.
was = aa56x50->get_CA_location();
p.rotate_piece(n56x50,
(type6 == Swing6) ? n6x55 : n6x59,
(type6 == Swing6) ? (or6abpy ? n6x57 : n6x55) : n6x59,
((type6 == Swing6) ? aa6x55 : aa6x48)->get_CA_location(),
axis6, theta6);
cout << "TMR6 rotation about " << *((type6 == Swing6) ? aa6x55 : aa6x48) << " by " << (theta6*fiftyseven) << "deg." << endl;
Expand Down Expand Up @@ -786,6 +800,13 @@ int main(int argc, char** argv)
cout << "Bridged 6.55 and 45.51." << endl;
}

if (or6abpy)
{
aa5x39->movability = aa6x57->movability = MOV_FLEXONLY;
p.bridge(n5x39, n6x57);
aa5x39->movability = aa6x57->movability = MOV_PINNED;
}


////////////////////////////////////////////////////////////////////////////////
// TMR5-TMR7 cytoplasmic side contact.
Expand Down