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Questions and answers > General discussions (Q&As)
buggy rebuild
lukeczapla:
Thank you. I had to play tricks with reverse_stnd2() and the spacings in the PDB prints to make something that a viewer could read. So if you could implement that support for the PDBx/mmCIF format, then I won't have to remove all the CONECT records for it to view properly. It is well intentioned and I want to make a web system that can simulate and visualize these really long DNA molecules and include 3DNA in the pipeline.
Thanks again.
xiangjun:
Wait until tomorrow to check back. The standard mmCIF format is the way to go for really long DNA molecules.
Xiang-Jun
xiangjun:
Hi Luke,
I've updated 3DNA to v2.3.1-2017jun24. It features the new --cif (or --mmcif) option in rebuild/fiber to output generated structures in the standard PDBx/mmCIF format. The previous largely unused -xml option for PDBML format output has been removed.
With the new option shown below,
--- Code: ---rebuild -cif -atomic structure-5000bp-ID0-B0-1.dat big-str.cif
--- End code ---
your structure would be like the attached image (created with Jmol).
Have a try, and please report back if it works as expected.
Xiang-Jun
lukeczapla:
Thank you Xiang-Jun, that was exactly what I was looking to see. A 5000 bp circular "mini-chromosome" with no proteins bound to it. I will work to integrate PDBx/mmCIF into my work, UCSF Chimera definitely reads it in and I have to ask the guys at 3Dmol about loading it into the browser with their JavaScript viewer. Do you have some special way to place the phosphates and sugar in rebuild? I'd like to try to understand it better and see where it lines up for nucleosome-bound DNA that has a lot of slide. I understand that you are more interested in the study of RNA structures in your research.
Thanks
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.
