Kristof Van Hecke wrote:
I want to optimize a DNA-helix with the function "Structure
idealisation" in Refmac_5.5.00782 (CCP4_6.1.1).
My question, is this performing just a geometry optimization (against
a library), or is there also an energy-optimization of some kind
involved,..?
What's the difference?
And according to the number of cycles (default 10) used, different
structural results are obtained, hence is there a means of estimating
the ideal number of cycles to use..?
I generally keep re-inputting the output PDB back into refmac until the
input and output PDB files are "identical" to, say, withing 0.001 A.
This is my definition of "convergence". It is important to use a small
number of cycles for each run because if you don't atoms can move far
enough to start "bumping" into atoms that were not close enough to
trigger a "bump" restraint at the beginning. At least, this is how it
was back in "my day".
-James Holton
MAD Scientist
