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Messages - wolson

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The 3DNA webserver is working.

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The hangup on your submission is likely related to the nature of the unusual bases treated in your system. The 3DNA webserver is working. You may want to try the new DSSR software to treat systems with unusual bases. These are not treated as rigorously in the 3DNA code. DSSR reports the rigid-body parameters, torsion angles, virtual distances, etc. found with 3DNA. You can download the software and learn about these and other features of DSSR from our 2015 NAR paper and the DSSR Manual (see links on the forum pages).

3
Hi, Xiang-Jun.

While the structures may appear to be identical at the level of successive base pairs, the backbone connections/directions differ. The direction is clear from the color-coding of bases and strands in the attached images. Look, for example, at the different pathways of the red, blue, yellow, green base sequence on the red strand.

Best,
w
 

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According to their 3DNA output files, all four of the attached structures have the same positive rise (+3.4 A), the PP and MM files have the same positive twist (+36 deg), and the PM and MP files have the same negative twist (-36 deg). The structures should have all four possible combinations of the signs for rise and twist, i.e., (+3.4, +36) for PP, (–3.4, -36) for MM, (+3.4, -36) for PM, and (-3.4, +36) for MP.

The error is related to the implementation of the Cambridge Convention in the computation of base-pair step parameters in 3DNA. Users interested in structures like these are interested in rigid-body parameters that reproduce the input structures rather than adhering to the Convention.

A useful option for such users would be the option NOT to follow the Cambridge Convention.

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Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.