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Topic: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Replies: 148 Last Post: May 8, 2012 3:40 AM

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Halitsky

Posts: 600
Registered: 2/3/09

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Posted: Apr 14, 2012 7:19 PM

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Below are the data for the two new correlations for the c2 (NADP-
binding) fold. Although there is still some unruliness in the data
(at the length interval extremities 13-22, 93-102, and 103-112), the
basic pattern we've seen from the last two folds seems to be holding
up fairly well. It will now be interesting to see if the remaining
three folds manifest the pattern at substantially the same level that
we've seen, or if the coefficients jump. I suspect that at least for
the c1 (TIM-Barrel) fold, the coefficients WILL jump (because this
fold is so very "regular", but I'm not going to bet my day job on
it ... )

c/e c/u
vs vs
Len c/L c/L
Int N Coeff Sig Coeff Sig
13-22 399 0.515 1.8E-28 0.589 1.4E-38
23-32 388 0.672 2.2E-52 0.707 6.3E-60
33-42 283 0.722 7.4E-47 0.701 3.7E-43
43-52 232 0.631 3.5E-27 0.640 4.4E-28
53-62 200 0.651 1.6E-25 0.659 2.8E-26
63-72 170 0.589 3.1E-17 0.685 6.6E-25
73-82 158 0.645 5.8E-20 0.671 5.5E-22
83-92 131 0.539 3.0E-11 0.633 5.2E-16
93-102 119 0.563 1.8E-11 0.475 1.8E-08
103-112 110 0.573 6.4E-11 0.554 3.5E-10

Date

Subject

Author

4/1/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/3/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Ray Koopman

4/3/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/6/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Ray Koopman

4/6/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/6/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/7/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Ray Koopman

4/7/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/8/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Ray Koopman

4/8/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/9/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/9/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/9/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Ray Koopman

4/9/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/9/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/10/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Ray Koopman

4/10/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/11/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/11/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Ray Koopman

4/11/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/11/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/11/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/11/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Art Kendall

4/11/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/13/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Ray Koopman

4/13/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/13/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/14/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Ray Koopman

4/14/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/14/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/14/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/14/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/14/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/15/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Ray Koopman

4/15/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/15/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/15/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Ray Koopman

4/16/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/16/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/16/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Ray Koopman

4/16/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/16/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/16/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/16/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/17/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Ray Koopman

4/17/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/17/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Ray Koopman

4/18/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/19/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Ray Koopman

4/19/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/20/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Ray Koopman

4/20/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/20/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/20/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/20/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/20/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/20/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Ray Koopman

4/20/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/20/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Ray Koopman

4/20/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/20/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/20/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

gimpeltf@hotmail.com

4/20/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

gimpeltf@hotmail.com

4/20/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

gimpeltf@hotmail.com

4/21/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

gimpeltf@hotmail.com

4/21/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/24/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Ray Koopman

4/22/12

Our first control group result is precisely how we want AML's program
to behave with control group data ....

Halitsky

4/23/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Halitsky

4/24/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Ray Koopman

4/24/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Halitsky

4/24/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Halitsky

4/24/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Ray Koopman

4/26/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Ray Koopman

4/26/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Halitsky

4/26/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Halitsky

4/27/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Ray Koopman

4/27/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Halitsky

4/27/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Ray Koopman

4/28/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Halitsky

4/28/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Ray Koopman

4/28/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Halitsky

4/28/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Ray Koopman

4/28/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

gimpeltf@hotmail.com

4/28/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Ray Koopman

4/28/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

gimpeltf@hotmail.com

4/28/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Halitsky

4/29/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Ray Koopman

4/29/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Ray Koopman

4/29/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Halitsky

4/29/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Ray Koopman

4/29/12

Your questions go to the "moment of truth" that Jacques and Arthur
may shortly be facing

Halitsky

4/29/12

Re: Your questions go to the "moment of truth" that Jacques and
Arthur may shortly be facing

Halitsky

4/29/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Halitsky

4/30/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Ray Koopman

4/30/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Halitsky

4/30/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Halitsky

4/30/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Ray Koopman

4/30/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Halitsky

4/30/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Ray Koopman

4/30/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Halitsky

5/1/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Ray Koopman

5/1/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Halitsky

5/1/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Ray Koopman

5/1/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Halitsky

5/1/12

Results for c1 study and control groups when model run WITHOUT the
four cells for shortest length interval 33-42

Halitsky

5/2/12

Results on c2 fold confirm peculiarity of length interval 33-42 seen
in c1 fold results

Halitsky

5/2/12

Model with adjusted weighting logic now works on c2 fold! (but PLEASE
review my new weighting logic !)

Halitsky

5/2/12

Actually, your original suggestion (input counts) works as well as
what I just posted for the c2 fold

Halitsky

5/3/12

Re: Actually, your original suggestion (input counts) works as well
as what I just posted for the c2 fold

Ray Koopman

5/3/12

Re: Actually, your original suggestion (input counts) works as well
as what I just posted for the c2 fold

Halitsky

5/3/12

Comparative results for {lnL,w,lnLw,x1,x2} & {lnL,w,lnLw,x1,x2,lnLx1,lnLx2}

Halitsky

5/4/12

Re: Comparative results for {lnL,w,lnLw,x1,x2} & {lnL,w,lnLw,x1,x2,lnLx1,lnLx2}

Ray Koopman

5/4/12

Re: Comparative results for {lnL,w,lnLw,x1,x2} & {lnL,w,lnLw,x1,x2,lnLx1,lnLx2}

Halitsky

5/4/12

Your question re significance of proportion involving counts of
01:10:01:11 inputs to Arthur's program

Halitsky

5/4/12

Results of both chi-square tests on all six folds

Halitsky

5/4/12

Re: Comparative results for {lnL,w,lnLw,x1,x2} & {lnL,w,lnLw,x1,x2,lnLx1,lnLx2}

Halitsky

5/4/12

I'm sending the a1 CI table off-line, since the format didn't hold here.

Halitsky

5/5/12

Re: I'm sending the a1 CI table off-line, since the format didn't
hold here.

Halitsky

5/5/12

Re: I'm sending the a1 CI table off-line, since the format didn't
hold here.

Ray Koopman

5/5/12

Re: I'm sending the a1 CI table off-line, since the format didn't
hold here.

Halitsky

5/7/12

Re: I'm sending the a1 CI table off-line, since the format didn't
hold here.

Halitsky

5/7/12

Re: I'm sending the a1 CI table off-line, since the format didn't
hold here.

Halitsky

5/8/12

Re: I'm sending the a1 CI table off-line, since the format didn't
hold here.

Ray Koopman

5/8/12

Re: I'm sending the a1 CI table off-line, since the format didn't
hold here.

Halitsky

5/6/12

Re: I'm sending the a1 CI table off-line, since the format didn't
hold here.

Ray Koopman

5/3/12

Could I ask you to check this 1st test using sum of chi-squares from
study vs control cells ?

Halitsky

5/3/12

Re: Could I ask you to check this 1st test using sum of chi-squares
from study vs control cells ?

Ray Koopman

5/3/12

Re: Could I ask you to check this 1st test using sum of chi-squares
from study vs control cells ?

Halitsky

5/3/12

Could I ask you to check this 1st test using converged likelihoods
for study/control/pooled runs?

Halitsky

5/3/12

Re: Could I ask you to check this 1st test using converged
likelihoods for study/control/pooled runs?

Ray Koopman

5/3/12

Re: Could I ask you to check this 1st test using converged
likelihoods for study/control/pooled runs?

Halitsky

5/1/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Halitsky

4/27/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Halitsky

4/28/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Ray Koopman

4/28/12

Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Halitsky

4/24/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Ray Koopman

4/19/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/20/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Ray Koopman

4/16/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/16/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Ray Koopman

4/16/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/14/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Ray Koopman

4/13/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Halitsky

4/8/12

Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Ray Koopman

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