Hi Bob
Yes, it's working perfectly. Thanks!
Note: new p1 is different than old p1 (as you said) but it does not match p11
This is with 14.4.0_2015.10.13 application
rotaProt = compare( {*.CA/2.1 & polymer=8} {*.CA/1.1 & polymer=8} );
show rotaProt;
// rotaProt =
[[-0.7424616,0.2323488,-0.6283032,132.39798],[0.14965674,0.9717479,0.1
8250754,65.91373],[0.6529577,0.04147502,-0.756258,41.888985],[0.0,0.0,0
.0,1.0]]
p1 = {112.7159 -1.6228517 -76.52575};
p2 = {67.10559 -0.5669861 -24.276031};
draw li @p1 @p2;
m3 = rotaProt%1;
t = rotaProt%2;
show m3;
// m3 =
[[-0.7424616,0.2323488,-0.6283032],[0.14965674,0.9717479,0.18250754],[
0.6529577,0.04147502,-0.756258]]
show t;
// t = {132.39798 65.91373 41.888985}
p11 = m3 * p1 + t;
show p1;
// p1 = {-35.98292 1.3251648 131.40462}
show p11;
// p11 = {96.415054 67.23889 173.29361}
p21 = m3 * p2 + t;
show p2;
// p2 = {-34.702354 5.061278 62.15254}
show p21;
// p21 = {97.695625 70.975006 104.04152}
draw li2 @p11 @p21
select 2.1;
rotate selected @rotaProt;
// both protein and "li2" line object are moved the same
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