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General discussions (Q&As) /
« on: April 12, 2007, 12:21:05 am »
Hi,
There is a default cut-off threshold (0.6) used in 3DNA to decide if a structure is too curved to calculate the global parameters based on C1'-C1' vector. It is defined in the file "misc_3dna.par" (under directory $X3DNA/BASEPARS) on the 7th line -- increase the value (based on your data) will make 3DNA output the parameters you request.
Needless to say, the file "misc_3dna.par" is a bit cryptic -- the parameters were added while 3DNA was under actively development. In the coming new release of 3DNA v2.0, the file is much easer to understand, as show below.
HTH,
Xiang-Jun
There is a default cut-off threshold (0.6) used in 3DNA to decide if a structure is too curved to calculate the global parameters based on C1'-C1' vector. It is defined in the file "misc_3dna.par" (under directory $X3DNA/BASEPARS) on the 7th line -- increase the value (based on your data) will make 3DNA output the parameters you request.
Needless to say, the file "misc_3dna.par" is a bit cryptic -- the parameters were added while 3DNA was under actively development. In the coming new release of 3DNA v2.0, the file is much easer to understand, as show below.
Code: [Select]
# Section 4: is this double helix curved?
std_curved: 0.6 # criterion to decide if a helix is curved (0.6)
HTH,
Xiang-Jun