Download R2R user manual - The Breaker Lab

circle used in optimizing the multistem junction will be used. circle-center must be first
in the list if it is used. (See demo/THF/THF.sto for an example of its use.)
If angle is the letter h, then alignment is horizontal. If it’s v, then alignment is vertical.
• try harder
Try harder to solve the problem, by trying different initial values of certain variables, and
seeing which leads to the best solution. The variables modified are initial radius and
initial first point angle (see below).
For multistem junction circular solver, I have encoded a few different values that have
worked in some circumstances. The list is, of course, not complete.
For the ... bulgecircley ... commands, I have not come upon any cases with a strong
need for alternate values. Therefore, try harder has no effect on these commands.
• initial radius number
Specifies the circle radius (in inches) that the solver will use as an initial value in its optimization. The starting values of variables can make a big difference in whether the optimizer
ends up with a good solution, an acceptable but not ideal solution or a complete mess. Sometimes you can get good starting values (where necessary) from less-constrained problems that
the computer has solved. The computer will output the optimal circle radius after solving a
problem. The default is 0.459181.
Note: I have considered trying to set initialization values like this using the simpler multistem junction circular function. However, this function won’t take into account var backbone range regions, whose lengths can be changed, so it won’t be a general solution.
• initial first point angle number
(Only applicable to multistem junction circular solver.) Specifies an angle in degrees
of a nucleotide immediately 50 to the right nucleotide in the enclosing base pair. The solver
will use this angle as an initial value in the optimization. The starting values of variables can
make a big difference in whether the optimizer ends up with a good solution, an acceptable
but not ideal solution or a complete mess.
Sometimes you can get good starting values (where necessary) from less-constrained problems
that the computer has solved. The computer will output the optimal first angle value after
solving a problem. The default is 70.
• initial var backbone length label length
Set an initial value for the variable-length backbone length, to help the optimizer reach
a good solution. label must specify the first label used in the var backbone range command, as described under fixed var backbone length, above. length is specified in units
of internucleotideLen (default: 0.105 inches), and can be any real number. However, the
solver will constrain it to be at least 1. The default initial length value is 2.
All commands will optionally append to a file a multistem junction bulgey command that
statically models the layout determined by the solver. This will happen if the R2R DUMP FILE shell
environment variable is set, and this environmental variable specifies the path to the file.
With solver, the computer will print some additional diagnostics. It will tell you the coordinates of the center of the circle and its radius (mainCircle =). Note: these coordinates are in
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