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Amber-MD / cpptraj

Biomolecular simulation trajectory/data analysis.
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nastruct: skip 0 values? *X-disp Y-disp h-Rise Incl. Tip h-Twist) #120

Closed hainm closed 9 years ago

hainm commented 9 years ago

I've just compared cpptraj and x3dna output. So far the helical pars match very well. But cpptraj skips 0.0 values for X-disp Y-disp h-Rise Incl. Tip h-Twist in Dataset. Is this your intention?

x3dna

#        Shear    Stretch   Stagger   Buckle   Prop-Tw   Opening     X-disp    Y-disp    h-Rise    Incl.     Tip     h-Twist
g-c     -0.158     0.029     0.330    -2.130    -3.117     0.386     0.000     0.000     0.000     0.000     0.000     0.000
drroe commented 9 years ago

@hainm Not sure what you mean here - can you give an example, preferably with files I can use to reproduce? Thanks.

hainm commented 9 years ago

@drroe this is pdb file: https://github.com/Amber-MD/pytraj/blob/master/tests/data/Test_NAstruct/x3dna/rna.pdb

this is output from x3dna for helical pars: https://github.com/Amber-MD/pytraj/blob/master/tests/data/Test_NAstruct/x3dna/bp_helical.par

pytraj took the data from DatasetList and it seems to me that cpptraj skip the 0 values for first g-c (non-capitalized) pairs for X-disp Y-disp h-Rise Incl. Tip h-Twist

drroe commented 9 years ago

This is actually a non-issue. Cpptraj isn't skipping anything - the calculation of helical parameters requires two basepair reference frames (similar to basepair step). So there really should only be 7 values.

hainm commented 9 years ago

okie. Just want to make sure.