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RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?
« Last post by xiangjun on Yesterday at 09:19:56 pm »Hi Gengshi,
I've checked the two PDB files you uploaded: a standard B-DNA model (ending with aligned2Z.pdb), and its mirror-image (L-DNA), with x-coordinates negated (ending with aligned2Z_i_x.pdb). For clarity, I've extracted the first 6 atoms from each file, so readers easily see the differences.
Mathematically, this is a simple operation, but you have created a hypothetical DNA type that is unknown to DSSR. Nevertheless, DSSR is functioning as intended:
Yes, that is correct. DSSR can see this is a left-handed helix, but it (currently) does not recognize your L-DNA form.
Along the line, one could imagine another form where y-coordinates are flipped. What would it be called? How would DSSR suppose to classify it?
In principle, yes. One just needs to incorporate the domain-specific knowledge into the DSSR code. I need to know more about your L-DNA before considering how to do that.
Best regards,
Xiang-Jun
I've checked the two PDB files you uploaded: a standard B-DNA model (ending with aligned2Z.pdb), and its mirror-image (L-DNA), with x-coordinates negated (ending with aligned2Z_i_x.pdb). For clarity, I've extracted the first 6 atoms from each file, so readers easily see the differences.
# a standard B-DNA model x
ATOM 1 P DA A 1 0.621 9.421 -1.028 1.00 0.00 P
ATOM 2 O1P DA A 1 0.606 10.783 -1.583 1.00 0.00 O
ATOM 3 O2P DA A 1 1.439 9.186 0.166 1.00 0.00 O
ATOM 4 O5' DA A 1 -0.863 8.945 -0.676 1.00 0.00 O
ATOM 5 C5' DA A 1 -1.693 8.405 -1.689 1.00 0.00 C
ATOM 6 C4' DA A 1 -2.528 7.255 -1.154 1.00 0.00 C
# a mirror-image, with x-coordinates negated
ATOM 1 P DA A 1 -0.621 9.421 -1.028 1.00 0.00 P
ATOM 2 O1P DA A 1 -0.606 10.783 -1.583 1.00 0.00 O
ATOM 3 O2P DA A 1 -1.439 9.186 0.166 1.00 0.00 O
ATOM 4 O5' DA A 1 0.863 8.945 -0.676 1.00 0.00 O
ATOM 5 C5' DA A 1 1.693 8.405 -1.689 1.00 0.00 C
ATOM 6 C4' DA A 1 2.528 7.255 -1.154 1.00 0.00 C
Mathematically, this is a simple operation, but you have created a hypothetical DNA type that is unknown to DSSR. Nevertheless, DSSR is functioning as intended:
- For the standard B-DNA model, DSSR classifies the dinucleotide step as 'B' correctly.
- For the L-DNA, DSSR cannot classify the dinucleotide steps. and designates them as '.' (see the section below). Also as noted in the header section, DSSR only recognizes the common A-, B-, and Z-form helices.
Note: a helix is defined by base-stacking interactions, regardless of bp
type and backbone connectivity, and may contain more than one stem.
helix#number[stems-contained] bps=number-of-base-pairs in the helix
bp-type: '|' for a canonical WC/wobble pair, '.' otherwise
helix-form: classification of a dinucleotide step comprising the bp
above the given designation and the bp that follows it. Types
include 'A', 'B' or 'Z' for the common A-, B- and Z-form helices,
'.' for an unclassified step, and 'x' for a step without a
continuous backbone.
--------------------------------------------------------------------
helix#1[1] bps=40
strand-1 5'-AAAAAAAAAATTTTTTTTTTCCCCCCCCCCGGGGGGGGGG-3'
bp-type ||||||||||||||||||||||||||||||||||||||||
strand-2 3'-TTTTTTTTTTAAAAAAAAAAGGGGGGGGGGCCCCCCCCCC-5'
helix-form .......................................
Quote
1. Is my understanding correct that DSSR can identify the geometry but does not recognize the form of our L-DNA?
Yes, that is correct. DSSR can see this is a left-handed helix, but it (currently) does not recognize your L-DNA form.
Along the line, one could imagine another form where y-coordinates are flipped. What would it be called? How would DSSR suppose to classify it?
Quote
2. Is there any way to make DSSR recognize the form of our L-DNA?
In principle, yes. One just needs to incorporate the domain-specific knowledge into the DSSR code. I need to know more about your L-DNA before considering how to do that.
Best regards,
Xiang-Jun