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Questions and answers > General discussions (Q&As)
buggy rebuild
lukeczapla:
I tried to rebuild this structure (base-pair step parameters) and it comes out as junk. The first base-pair is not even in the standard reference frame near the origin. It does this in both v2.1 and v2.3.
command:
rebuild -atomic structure-5000bp-ID0-B0-1.dat out.pdb
Thanks
Luke Czapla
xiangjun:
Hi Luke,
This is not a bug in rebuild but related to the limitation of the classic PDB format. You can easily verify this by checking the outputted PDB file. By reducing the number of base pairs (say to 500) in your input, you can get an expected structure in the PDB format.
Try the -xml option to output the desired structure in PDBML format, as shown below:
--- Code: ---rebuild -atomic -xml structure-5000bp-ID0-B0-1.dat big-str.xml
--- End code ---
HTH,
Xiang-Jun
lukeczapla:
It's more than just the numbers, something's really going wrong with your code, here's the first nucleotide (which should be at the origin), and in v2.3 it's exactly the same:
REMARK 3DNA v2.1-2014mar25, created and maintained by Xiang-Jun Lu (PhD)
ATOM 1 C1' A A 1 1962.0311187.0561104.807 1.00 1.00 C
ATOM 2 N9 A A 1 1963.2191186.2081104.807 1.00 1.00 N
ATOM 3 C8 A A 1 1964.5341186.6071104.807 1.00 1.00 C
ATOM 4 N7 A A 1 1965.3871185.6121104.807 1.00 1.00 N
ATOM 5 C5 A A 1 1964.5811184.4811104.807 1.00 1.00 C
ATOM 6 C6 A A 1 1964.8791183.1081104.807 1.00 1.00 C
ATOM 7 N6 A A 1 1966.1211182.6191104.807 1.00 1.00 N
ATOM 8 N1 A A 1 1963.8421182.2421104.807 1.00 1.00 N
ATOM 9 C2 A A 1 1962.5981182.7331104.807 1.00 1.00 C
ATOM 10 N3 A A 1 1962.1901184.0001104.807 1.00 1.00 N
ATOM 11 C4 A A 1 1963.2431184.8341104.807 1.00 1.00 C
But it's fine, if you don't want to fix it, I can use my own code to rebuild the DNAs. Most programs don't seem to support this XML format. It's really a simple fix, just output 2 decimals, it will be properly read in Chimera, VMD, and 3Dmol.
xiangjun:
Did you notice the diagnostic message when running 'rebuild' when the structure is big? The coordinates are reset to account for f8.3 format. To verify if 'rebuild' is doing what it is supposed to do, simply 'analyze' the generated structures. It should give the parameters you start with.
So far, I am not convinced "something is really going wrong" with analyze/rebuild. What to fix? Everything is working as expected, from my perspective. It is nice to have open discussions, on the 3DNA Forum.
Xiang-Jun
lukeczapla:
if it had a flag to handle big numbers using %8.2f or %8.1f and override what you believe to be the only "correct" way to write a PDB file, that'd make it compatible with the common applications that are used to visualize systems and generate images, which don't agree with you that that's the only correct way to format a number in a PDB file. So it's not that it's wrong, it's just that it's not flexible with these larger datasets and the reality of using the product for research.
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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.
