just SO3 test; update full model (SE3) to note that discrepancy is no…

…t too bad

notes/ToyFold3D_NOTES.rtfd/TXT.rtf

@@ -287,32 +287,42 @@ And for 2-mr [cyclic dinucleotide] there may be only one solution:\
 \cf0 \
 \
 \
-\ul Let\'92s work through how to do KDE\'92s for SO(3) \
-\ulnone Check volume element.\
+\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\pardeftab560\pardirnatural\partightenfactor0
+\cf0 \ul Let\'92s work through how to do KDE\'92s for SO(3) \
+\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\pardeftab560\pardirnatural\partightenfactor0
+\cf0 \ulnone Check volume element.\
+\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\pardeftab560\pardirnatural\partightenfactor0
 
-\i check_rotations_test. 
+\i \cf0 check_rotations_test. 
 \i0 [copied from loop_close/ GitHub repo]\
 \
 Use \ul SpinCalc\ulnone  to generate\
 
 \i \
-\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardirnatural\partightenfactor0
+\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
 
 \i0 \cf0 {{\NeXTGraphic Screen Shot 2020-06-02 at 1.29.30 PM.png \width7800 \height7240
-}¬}{{\NeXTGraphic Screen Shot 2020-06-02 at 1.29.26 PM.png \width7640 \height6720
-}¬}{{\NeXTGraphic Screen Shot 2020-06-02 at 1.29.34 PM.png \width10180 \height7980
-}¬}\
+}¬}\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
+\cf0 {{\NeXTGraphic Screen Shot 2020-06-02 at 1.29.26 PM.png \width7640 \height6720
+}¬}\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
+\cf0 {{\NeXTGraphic Screen Shot 2020-06-02 at 1.29.34 PM.png \width10180 \height7980
+}¬}\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
+\cf0 \
 \
 \
 \
 OK!\
-\ul How does KDE do?\
-\ulnone Depends on number of samples. Interestingly, overestimates/underestimates depending on number of samples, which seems OK.\
-\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardirnatural\partightenfactor0
+\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
+\cf0 \ul How does KDE do?\
+\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
+\cf0 \ulnone Depends on number of samples. Interestingly, overestimates/underestimates depending on number of samples, which seems OK.\
+\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
 \cf0 {{\NeXTGraphic Screen Shot 2020-06-02 at 1.50.50 PM.png \width7080 \height9500
-}¬}{{\NeXTGraphic Screen Shot 2020-06-02 at 1.50.44 PM.png \width6980 \height9420
-}¬}{{\NeXTGraphic Screen Shot 2020-06-02 at 1.50.37 PM.png \width6960 \height9620
-}¬}\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardirnatural\partightenfactor0
+}¬}\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
+\cf0 {{\NeXTGraphic Screen Shot 2020-06-02 at 1.50.44 PM.png \width6980 \height9420
+}¬}\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
+\cf0 {{\NeXTGraphic Screen Shot 2020-06-02 at 1.50.37 PM.png \width6960 \height9620
+}¬}\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
 \cf0 \
 In bottom panels above, also tried b transform to make space uniform:\
 \
@@ -323,22 +333,22 @@ Note systematic downturn at high rotation vectors, due to boundary effects at ed
 So just try to do KDE, dividing by (1/8pi^2) x sinc(v/2)^2. This corrects for downturn at high rotation vectors to give \'91true\'92 probability density per phase space volume,  dp/domega.\
 \
 OK updated my KDE overlap code for circularization \'97 better agreement between overlap-based calcs and return-to-origin calcs, which used to be off by ~2x!:\
-\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardirnatural\partightenfactor0
+\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
 \cf0 {{\NeXTGraphic Screen Shot 2020-06-02 at 2.17.55 PM.png \width11120 \height5380
-}¬}\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardirnatural\partightenfactor0
+}¬}\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
 \cf0 \
-\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardirnatural\partightenfactor0
+\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
 \cf0 {{\NeXTGraphic Screen Shot 2020-06-02 at 2.17.43 PM.png \width10940 \height5460
-}¬}\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardirnatural\partightenfactor0
+}¬}\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
 \cf0 \
 \
-\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardirnatural\partightenfactor0
+\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
 \cf0 {{\NeXTGraphic Screen Shot 2020-06-02 at 2.18.10 PM.png \width10800 \height5420
-}¬}\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardirnatural\partightenfactor0
+}¬}\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
 \cf0 \
-\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardirnatural\partightenfactor0
+\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
 \cf0 {{\NeXTGraphic Screen Shot 2020-06-02 at 2.17.24 PM.png \width11380 \height5380
-}¬}\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardirnatural\partightenfactor0
+}¬}\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
 \cf0 \
 \
 Though there\'92s still a systematic underestimation based on overlap. \
@@ -347,17 +357,67 @@ Is distribution too \'91spiky\'92 to be handled well by multivariate KDE? Lots o
 * Check if re-centering helps?\
 * Another cross-check \'97> create samples based on multi-jointed chain, where I know answer analytically from Fourier transforms.\
 * Note that circularize to origin may also be biased to be high. Probably only way to check would be lots of compute and grid-based calculations, rather than KDE.\
-\
 \pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardirnatural\partightenfactor0
-\cf0 Also tried isometric v->b transformation before KDE. Nope \'97 leads to even *worse* underestimation. So turn off that \'91isometric\'92 flag in 
+\cf0 \
+\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
+\cf0 \
+Also tried isometric v->b transformation before KDE. Nope \'97 leads to even *worse* underestimation. So turn off that \'91isometric\'92 flag in 
 \f3\fs20 get_C_eff_from_pts_6D
 \fs24 \
 
 \f2 \
-\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardirnatural\partightenfactor0
+\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
 \cf0 {{\NeXTGraphic Screen Shot 2020-06-02 at 2.31.28 PM.png \width10020 \height8040
-}¬}\
+}¬}\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
+\cf0 \
+\
+\
+\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
+\cf0 \
+Actually rerun above with lots of replicates\'96 after some bug fixes caught below \'97 its not too bad!\
+\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
+\cf0 {{\NeXTGraphic Screen Shot 2020-06-06 at 7.46.56 PM.png \width13440 \height6720
+}¬}\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
+\cf0 \
+\
+\
+For 10-mer \'97 actually not too bad \'97 biggest error is 1<\'97>9. \
+\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
+\cf0 \
+\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardirnatural\partightenfactor0
+\cf0 {{\NeXTGraphic Screen Shot 2020-06-06 at 7.53.34 PM.png \width13280 \height6740
+}¬}\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardirnatural\partightenfactor0
+\cf0 \
+\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
+\cf0 \
+\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
+\cf0 \ul 6 June, 2020\
+just_so3_test.m\
+\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
+\cf0 \ulnone How about just  SO(3) part? Can we isolate the issue?\
+\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
+\cf0 \ul \ulc2 \
+\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardeftab560\pardirnatural\partightenfactor0
+\cf0 \ulnone \
 \pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\pardeftab560\pardirnatural\partightenfactor0
 \cf0 \
+\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardirnatural\partightenfactor0
+\cf0 {{\NeXTGraphic Screen Shot 2020-06-06 at 7.13.11 PM.png \width10180 \height8040
+}¬}\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardirnatural\partightenfactor0
+\cf0 {{\NeXTGraphic Screen Shot 2020-06-06 at 7.12.53 PM.png \width10580 \height8020
+}¬}\
 \
+Some variation, though look at axis limits \'97 not much (10-20%). \
+\
+Still, may be useful. Recompute 20-mer. Caught an error where sin(q/2)/(q/2) gives nan, throws off computation of last points (circularization of 20-mer forward or reverse, back to origin)\
+\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardirnatural\partightenfactor0
+\cf0 {{\NeXTGraphic Screen Shot 2020-06-06 at 7.28.39 PM.png \width10380 \height7920
+}¬}\
+Note how off first point is for red. Can sort of see why \'97 trying to compare a very concentrated distribution (red, R) and diffuse distribution (blue). But discrepancy is 
+\i opposite
+\i0  of problem in SE(3) where KDE overlap underestimates \'91true\'92 [?]. Also in different direction in repeat compared to original data.\
+\
+\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardirnatural\partightenfactor0
+\cf0 {{\NeXTGraphic Screen Shot 2020-06-06 at 7.28.31 PM.png \width9620 \height7840
+}¬}\
 }

runs/just_so3_test.m

@@ -0,0 +1,31 @@
+% Try to do projection for a 'pseudochain' that lives only in rotation
+% space SO(3)
+
+%% The rotation part of the SE(3) rotation/translation transform 
+% is just m' = R*m, same SO(3). So I can use prebuilt chains or transforms
+% for SE(3) if I just pull out the rotation vectors. 
+%load toyfold3_test.mat t R all_pts_f all_pts_r
+
+Nmax = 20; NITER = 1000;
+[all_pts_f, all_pts_r] = get_all_pts( Nmax, NITER, t, R );
+
+%% Show overlap
+figure(2)
+N = 20;
+just_SO3 = 1;
+[C_eff_overlap_f, C_eff_overlap_r] = get_C_eff_overlap( N, all_pts_f, all_pts_r, just_SO3 ); clf;
+plot( [C_eff_overlap_f; C_eff_overlap_r]' ); hold on   
+%plot( N,mean( C_eff(find(which_N==N)) ),'x' );  
+h = legend( 'C_eff_overlap_f','C_eff_overlap_r','overlap at 0'); set(h,'interpreter','none');
+set(gca,'fontweight','bold'); xlabel( 'n steps for overlap'); ylabel('C_{eff} (M)');
+title(sprintf('Forward/reverse overlap molarity for circularization of %d-mer',N) );
+set(gcf, 'PaperPositionMode','auto','color','white');
+
+%% take a look at the points.
+figure(3)
+pts = all_pts_f{19}(:,4:6);
+plot3( pts(:,1), pts(:,2), pts(:,3), '.' ); axis equal; axis vis3d
+hold on
+pts = all_pts_r{1}(:,4:6);
+plot3( pts(:,1), pts(:,2), pts(:,3), '.' ); axis equal; axis vis3d
+legend( 'F 19-mer','R 1-mer');

runs/toyfold3_test.m

@@ -14,7 +14,7 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %% Let's get some statistics, and estimate return probability 
 % (C_eff for circular RNA)
-which_N = [2:9 10:5:40, 2:9 10:5:40, 50:10:100]; NITER = 100000;
+which_N = [2:19 20:5:40, 2:19 20:5:40, 2:19, 2:19, 50:10:100]; NITER = 5000;
 %which_N = [2:12, 2:12]; NITER = 100000;
 C_eff = compute_C_eff_circular(NITER, which_N, t, R);
 %%
@@ -30,12 +30,12 @@
 [all_pts_f, all_pts_r] = get_all_pts( Nmax, NITER, t, R );
 
 %% Show overlap
-N = 10;
+N = 5;
 [C_eff_overlap_f, C_eff_overlap_r] = get_C_eff_overlap( N, all_pts_f, all_pts_r ); clf;
 plot( [C_eff_overlap_f; C_eff_overlap_r]' ); hold on   
 plot( N,mean( C_eff(find(which_N==N)) ),'x' );  
 h = legend( 'C_eff_overlap_f','C_eff_overlap_r','overlap at 0'); set(h,'interpreter','none');
-set(gca,'fontweight','bold'); xlabel( 'n steps for overlap'); ylabel('C_{eff} (M)');
+set(gca,'fontweight','bold','xgrid','on'); xlabel( 'n steps for overlap'); ylabel('C_{eff} (M)');
 title(sprintf('Forward/reverse overlap molarity for circularization of %d-mer',N) );
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -49,4 +49,5 @@
 plot( N_overlap, C_eff_overlap_halfway); hold on
 set(gca,'fontweight','bold');xlabel('N');ylabel('C_{eff} (M)');
 legend( 'circularize to origin','overlap of forward/reverse' );
+set(gcf, 'PaperPositionMode','auto','color','white');
 

scripts/C_eff/get_C_eff_from_pts_6D.m

@@ -1,9 +1,10 @@
-function C_eff = get_C_eff_from_pts_6D( pts_f, pts_r);
-% C_eff = get_C_eff_from_pts_6D( pts_f, pts_r);
+function C_eff = get_C_eff_from_pts_6D( pts_f, pts_r, just_SO3);
+% C_eff = get_C_eff_from_pts_6D( pts_f, pts_r, just_SO3);
 %
 % INPUTS
 %  pts_f = sampled (x,y,z,v_x,v_y_v_z) for forward chain segment
 %  pts_r = sampled (x,y,z,v_x,v_y,v_z) for reverse chain segment
+%  just_SO3 = only look at rotation part of translation+rotation;
 %
 % OUTPUT
 %  C_eff = Effective molarity for chain closure between forward samples
@@ -12,29 +13,35 @@
 %            MATLAB's KDE estimator.
 %
 % (C) R. Das, Stanford University, 2020
+if ~exist( 'just_SO3','var') just_SO3 = 0; end;
 
 isometric = 0; % leads to systematic underestimation
 if isometric
     pts_f = convert_v_to_b(pts_f);
     pts_r = convert_v_to_b(pts_r);
 end
+if just_SO3
+    pts_f = pts_f(:,4:6);
+    pts_r = pts_r(:,4:6);
+end
 
 s = get_kde_bandwidth( pts_f );
-
-% phase space factor for integration with euler vectors
-%  WAIT -- should I apply this or the inverse of it? 
-%  Think through this more.
-
-p = mvksdensity( pts_f, pts_r,'Bandwidth',s); 
+p = mvksdensity( pts_f, pts_r,'Bandwidth',s);
 
 if isometric
     C_eff = mean(p)/(1/(8*pi^2)*6.022e23/1e27 );
 else
     % correct for phase space volume
-    v = sqrt( sum(pts_r(:,4:6).^2, 2) ); % rotation angle
+    v = sqrt( sum(pts_r(:,end-2:end).^2, 2) ); % rotation angle
     w = (sin(v/2)./(v/2)).^2;
+    w( find( v == 0 ) ) = 1;
     C_eff = mean(p./(w/(8*pi^2)))/ (6.022e23/1e27);
 end
+if just_SO3
+    % don't need to conversion to molarity.
+    C_eff = C_eff * (6.022e23/1e27);
+end
+
 
 function b = convert_v_to_b(v);
 % isometric rescaling so uniform distribution in

scripts/C_eff/get_C_eff_overlap.m

@@ -1,4 +1,4 @@
-function [C_eff_overlap_f, C_eff_overlap_r] = get_C_eff_overlap( N, all_pts_f, all_pts_r );
+function [C_eff_overlap_f, C_eff_overlap_r] = get_C_eff_overlap( N, all_pts_f, all_pts_r, just_SO3 );
 % [C_eff_overlap_f, C_eff_overlap_r] = get_C_eff_overlap( N, all_pts_f, all_pts_r );
 %
 %
@@ -8,6 +8,7 @@
 %       [6 x NITER] points in 6D SE(3) space: x, y, z, v_x, v_y, v_z  
 %  all_pts_r = cell of Nmax arrays of reverse samples, each with 
 %       [6 x NITER] points in 6D SE(3) space: x, y, z, v_x, v_y, v_z  
+%  just_SO3 = only look at rotation part of translation+rotation;
 %
 % Outputs
 %
@@ -17,9 +18,10 @@
 %              reverse from 1, 2, ... N
 %
 % (C) R. Das, Stanford University 2020
+if ~exist( 'just_SO3','var') just_SO3 = 0; end;
 for i = 1:N-1
-    C_eff_overlap_f(i) = get_C_eff_from_pts_6D(all_pts_f{i},all_pts_r{N-i});
-    C_eff_overlap_r(i) = get_C_eff_from_pts_6D(all_pts_r{i},all_pts_f{N-i});
+    C_eff_overlap_f(i) = get_C_eff_from_pts_6D(all_pts_f{i},all_pts_r{N-i},just_SO3);
+    C_eff_overlap_r(i) = get_C_eff_from_pts_6D(all_pts_r{i},all_pts_f{N-i},just_SO3);
 end
-C_eff_overlap_f(N) = get_C_eff_from_pts_6D(all_pts_f{N},[0,0,0,0,0,0]);
-C_eff_overlap_r(N) = get_C_eff_from_pts_6D(all_pts_r{N},[0,0,0,0,0,0]);
+C_eff_overlap_f(N) = get_C_eff_from_pts_6D(all_pts_f{N},[0,0,0,0,0,0],just_SO3);
+C_eff_overlap_r(N) = get_C_eff_from_pts_6D(all_pts_r{N},[0,0,0,0,0,0],just_SO3);