Question about the axial length of B-DNA generated in ChimeraX
Dear ChimeraX Team, I am comparing B-DNA models generated in ChimeraX, 3DNA, and Coot, and noticed that the ChimeraX-built model is substantially shorter. For a 65-bp duplex with the same alternating AT sequence, the ChimeraX and 3DNA models give the following results: * 3DNA fiber model #4: axial advance of 3.375 Å per step and rotation of 36°, giving an axial span of approximately 216.0 Å over 64 steps. * ChimeraX-built B-DNA: axial advance of approximately 3.086 Å per step and rotation of approximately 35.708°, giving an axial span of approximately 197.5 Å. The ChimeraX model is therefore about 18.5 Å shorter. The B-DNA model generated in Coot is very similar in overall length to the 3DNA model, so the ChimeraX model appears shorter than both references. Rigid alignment does not remove this difference. Analysis of both coordinate files using the same version of 3DNA confirms the difference in global axial advance. I also checked the B.xform file in the ChimeraX release/v1.9 source, whose transformation appears consistent with the shorter axial increment. Could you please clarify the origin of the built-in B-DNA template and its intended helical parameters? Does it represent a particular experimental structure or published parameter set, and is this shorter axial advance expected? Any reference or guidance would be very helpful for choosing an appropriate B-DNA reference for structural comparisons. Thank you for your help. Junwei Li
Hi Junwei, The DNA parameters were derived by surveying the PDB for experimental DNA structures whose keywords indicate that the entry should contain a fairly regular double helix (i.e. “DOUBLE HELIX” is in the keywords, and things like “MODIFIED”, “MISMATCHED”, “DRUG-DNA COMPLEX” [and many others] are not). There were 53 such entries for B-DNA (file listing them attached). Then for each consecutive nucleotide triplet that is properly base paired to its complementary strand, the central nucleotide geometric parameters are extracted and compiled into lists that are then averaged to generate the parameters for building up a nucleotide backbone/sidechain. This is very much a 30,000-foot view — there are many, many sanity checks in the processing script before a particular triplet is used for parameters. So perhaps you could compare the 3DNA model and the ChimeraX model against some of these experimental models to judge which one is better for your purposes. --Eric Eric Pettersen UCSF Computer Graphics Lab 
On Oct 28, 2026, at 5:39 PM, Li, Junwei via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Team, I am comparing B-DNA models generated in ChimeraX, 3DNA, and Coot, and noticed that the ChimeraX-built model is substantially shorter. For a 65-bp duplex with the same alternating AT sequence, the ChimeraX and 3DNA models give the following results: 3DNA fiber model #4: axial advance of 3.375 Å per step and rotation of 36°, giving an axial span of approximately 216.0 Å over 64 steps. ChimeraX-built B-DNA: axial advance of approximately 3.086 Å per step and rotation of approximately 35.708°, giving an axial span of approximately 197.5 Å. The ChimeraX model is therefore about 18.5 Å shorter. The B-DNA model generated in Coot is very similar in overall length to the 3DNA model, so the ChimeraX model appears shorter than both references. Rigid alignment does not remove this difference. Analysis of both coordinate files using the same version of 3DNA confirms the difference in global axial advance. I also checked the B.xform file in the ChimeraX release/v1.9 source, whose transformation appears consistent with the shorter axial increment. Could you please clarify the origin of the built-in B-DNA template and its intended helical parameters? Does it represent a particular experimental structure or published parameter set, and is this shorter axial advance expected? Any reference or guidance would be very helpful for choosing an appropriate B-DNA reference for structural comparisons. Thank you for your help. Junwei Li _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (2)
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Eric Pettersen -
Li, Junwei