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Questions and answers > General discussions (Q&As)
buggy rebuild
xiangjun:
--- Quote ---what you believe to be the only "correct" way to write a PDB file
--- End quote ---
Well, I just follow the standard PDB format, and as shown in the PDB entries from the RCSB. I have no opinon on this matter at all.
On a practical side, the source code of 3DNA is available. One can easily change f8.3 to f8.2 or f8.1, as desired. However, that will NOT solved the inherent limitation of the classic PDB format.
Xiang-Jun
lukeczapla:
Believe me, if it was just changing a sprintf("%8.3f") to a sprintf("%8.2f") in your code, I would've done that already, I have the source. But with this whole operation you're performing (following that warning you mentioned, which I did see), it is not so simple. Therefore I just ended up writing my own code to rebuild double-stranded DNA. Correct me if I'm wrong though, because I will go and change it myself if it's that simple.
Thank you
xiangjun:
The thread has diverged from its original subject matter. To repeat my point, 3DNA 'rebuild' is working as designed, from v1.5 in 2003, upto the current v2.3. I may consider an option for PDBx/mmCIF output format, but the PDB format will stay as is.
I'm glad you've written your own code to build your DNA model. Good luck!
Xiang-Jun
lukeczapla:
Ok I think I fixed it. I changed a line in reset_xyz() function to not reset the bp unless it's bigger than 99999.9 or -99999.99 and then it really is just changing to %8.2. I should be good to go.
xiangjun:
Hi Luke,
Thanks for your feedback. I'm adding the --cif (or --mmcif) option to 'rebuild' and 'fiber' to handle large structures that cannot be accommodated by the classic PDB format. The --xml option was added in 3DNA before the PDBx/mmCIF format became the standard. As you noted, the PDBML (XML) format is seldomly implemented in common molecular viewers (including Jmol/PyMOL, as far as I have tested).
I'll release an updated 3DNA v2.3 when the coding of the --cif option is done. I've originally planed to add this feature to 3DNA v3. Since you've brought up this issue to my attention, I thought it'd be helpful to get it added in v2.3 as well.
Best regards,
Xiang-Jun
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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.
