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General discussions (Q&As) / PDBML output in 3DNA
« on: October 04, 2006, 09:59:12 am »
Hello, Xiang-Jun,
As you are aware, I use your 3DNA program to construct DNA models based on MD data at my website
http://humphry.chem.wesleyan.edu:8080/M ... Pages.html
When I construct some interesting but very long DNA structure (~15 KB), although 3DNA gives me a pdb format or alchemy format output file there is usually a coordinate overflow. This happens because of the pdb format lmitation of F8.3 (or F9.4? in alchemy) on the coordinate values in these files.
One alternative that might overcome this problem is if we can output the file in PDBML format instead of PDB.
Is there anyway we could work this out ? I will be glad to incorporate this extension in 3DNA.
Thanks.
Surjit
As you are aware, I use your 3DNA program to construct DNA models based on MD data at my website
http://humphry.chem.wesleyan.edu:8080/M ... Pages.html
When I construct some interesting but very long DNA structure (~15 KB), although 3DNA gives me a pdb format or alchemy format output file there is usually a coordinate overflow. This happens because of the pdb format lmitation of F8.3 (or F9.4? in alchemy) on the coordinate values in these files.
One alternative that might overcome this problem is if we can output the file in PDBML format instead of PDB.
Is there anyway we could work this out ? I will be glad to incorporate this extension in 3DNA.
Thanks.
Surjit