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Questions and answers > General discussions (Q&As)
'rebuild' and the f8.3 limit, 1014 bp circular structure
ry54451:
Please disregard my last post's question. If I start from x.par, I can do the rebuild and then find_pair to generate the ref. frame file.
I am running a new optimization. If I run into new occurrences where chucks are removed from the optimized circles I will follow-up on here.
Thanks for your assistance.
xiangjun:
I'm glad to hear that things are sorted out.
--- Quote ---Once I re-did what you did earlier (find_pair, cp_std, and then rebuild), I did not get any error, although the two .pdb models have a coordinate shift. My error seems to be with emDNA_parser and, therefore, not through you.
--- End quote ---
The "coordinate shift" is what the diagnostic message "xyz coordinate under f8.3 limit. reset origin to minimum xyz coordinates" is about. The "rebuild" program is simply resetting the center of the structure so that the atomic coordinates can be better fitted into the f8.3 limit of PDB format.
--- Quote ---However, is there a way to generate a reference frame file from a starting .par file using x3dna?
--- End quote ---
Did you notice that after running "rebuild", a file named "ref_frames.dat" is also generated? Presumably, that's what you are looking for.
Enjoy using 3DNA.
Xiang-Jun
ry54451:
Follow-up question for all of this:
I cannot find anything in documentation about this, but does 3DNA have a way to generate a .par file from a reference frame file?
I know I can go from .par to refframes.dat, but not the other way.
xiangjun:
No, not in the current 3DNA v2.3 version.
Could you please explain your use-case for such a functionality? I may be convinced to add it in later releases of 3DNA v2.3.
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.
