Monthly Archives: August 2022

Verge of a Dream: You better get a lesson –

You better get a lesson
From up that hill
From up that hill (refrain)

It all came down
Came down on me
May still come down
On you too
Still come Down
on you too


Wrap your body up
Flake’s not cold but
Won’t be one alone
Look up that hill.
At a million coming


What someone wise said
Wise for sure
You better better
Take what happened
To me, see that
See all that
try to listen well


It can’t be easy
Whether you make
The bread or find
Yourself in line.
Its just the same
a common
bramble vine or
a soul divine.

refrain repeated

RLB 08-09-2022

Four SP-D dodecamers: more plots use to determine trimer and hexamer peak numbers

Previously counted plots included all that were available at the time (found in this link; which had about equal numbers of plots from each dodecamer (hexamer – trimer). The data on this page show just about every plot that I have ever made….. these are divided as to trimer…. so this is mean trimer peak number. The latter counts the N term peak with each trimer (even though it is shared between all the trimers…. each trimer it gets counted once.   Therefore a peak number of 8 per trimer would become peak number of 15 per hexamer owing to the N term peak being shared.  In terms of progress…. its best to assume that the more recent posts are the better data.  Every possible image and signal processing filters and algorithms are summed here. Some people counts, all counts….  this represents a huge N, in my estimation.

I think my current favorite image processing filter is still the gaussian blur, and my favorite peak counting program is PeakValleyDetectionTemplate.xlsx by Thomas O’Haver.

Peaks per hexamer were calculated four ways.  As every plot made for each of these four dodecamers. This includes hundreds of counts for one dodecamer, and between 26 and 50 hexamer plots for the other three. Certainly one carries more weight, or one would think, but the data using each of the plots separately is not different than using each of the methodologies (at an absolute minimum there were 2 image processing filters, and at least 5 signal processing algorithms for several of these image processed pictures.

Data are also given with each of the four dodecamers individually: (41_ak45; 42a_aka_44; 43; 97-1).  In addition. n, mean, sd, and other parameters were calculated from my original peak counts from just the “image”, as well as from my original peak counts from the plot generated in ImageJ.  This is in addition to the whole lot of plots subjected to signal processing.    Bottom line is that signal processing appears to increase the peak count in a significant way. Whether the signal processing is “better” (which i dont think it true” or counts from images is “better” remains to be sorted out.   Below is a comparison of the various “sorting” that I used to determine mean number of peaks per hexamer of SP-D.

Two left columns are: 1) Every plot of a hexamer separately, 2) Plots divided into each of the four dodecamers separated into groups; Two right columns are counts separated into  “image with signal processing” per dodecamer ( and separated again into, my counts of image processing plots only plus my counts of the peaks in plots made in ImageJ (that is… NO SIGNAL processing)  18+ peaks with signal processed plots, and 15+ peaks using my hand counts.  15 peaks per hexamer is in my bet for the best number.  See previous posts here.


Getting closer to making a “concensus SP-D LUT plot” from which to build an AI model

Getting closer to making a “concensus SP-D LUT plot” from which to build an AI model.

I had four SP-D dodecamers to work with, literally hundreds of plots, 5 different plot peak finding algorithms (apps, programs, websites), and a dozen different image processing programs, all to find the perfect peak plot for SP-D hexamers.  These molecules are bilaterally symmetrical (three identical x three identical) with the N term junction in the center.  Little is known about the central connections though the CRD and neck regions have molecular models.  Taken about 3 years to try to figure this out, input would have been (would still be) very valuable.

I am hopeful that an easy technique will be the outcome, that is an easy technique for assessing peaks in many different types of molecules (images from AFM at this point), particularly those which are bilaterally symmetrical.

Out of 7.7 billion people

Out of 7.7 billion people, I marvel that I have not found ONE single one with whom I can share my interests, not in gardening, mosaic, stained glass, polymer clay art, science, electron microscopy, pattern making, music, writing music, repairing old houses, making walkways with concrete.  You would think at least ONE person would be around to do these things with.  Dunno…  what are the odds.

Verge of a Dream: Advice

I’ve heard it said
What seems like
Good instruction
be not attached
To things. So
maybe three
times or maybe
Passed it on to
Titan yet there,
all my lifetime,
it was, and is,
in orbit,
To Saturn.
I’ve heard it said,
And sensible it may
to forge your
Own trail cause
Convention will not
The mother of
Invention. Passed it
On to my captain
Who drew new plots
And graphs found
Board our
ship discovered
Lost at sea.
I’ve heard it said
And it seemed
The path
Of progression
to do things better,
as a gift
to the next
And now
mostly done with
Looking I wish
I’d followed
That connected
Me and you
Less to now
moored my
life to then.

RLB 7-31-2022