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Questions and answers > General discussions (Q&As)
'rebuild' and the f8.3 limit, 1014 bp circular structure
ry54451:
Hello all.
I'm currently working with a 1014bp circular sequence and generating a series of initial structures from a web-based Monte Carlo calculation. This platform allows me to generate and download a pdb file.
My problem is that of the 15 structures I've made, only 2 seem to have an issue during the 'rebuild' process that I use since the web-based pdb files are poly(A) and not of my particular sequence. One structure stays connected but the "rebuild" structure shows a chunk of the structure away from the rest of the circle and apparently flattened. (cannot attach pdb file due to file size).
I am still able to optimize the refframe files with no problem, but even the optimized pdb file for this particular structure has this chunk out.
And again, of my 15, only 2 have done. The structures range in Rg values, but the two with the issue happen to be in the middle of Rg values.
Current set-up: v2.3-2017feb08
- wishing to stay with .pdb files for the molecular modeling with PyMol.
Any suggestions to best rectify this?
xiangjun:
Given only the description in your post, it is impossible to decipher where the problem is. The title mentions the f8.3 limit of PDB format, would a 3DNA-rebuilt structure in mmCIF file help?
Please clarify.
Xiang-Jun
ry54451:
I'm not sure how best to clarify my problem. My apologies.
As for the mmCIF formatting, I do not know if that is a file format I know how best to use by I can certainly give that a try.
xiangjun:
On what platform (Windows, macOS, or Linux) did you run 3DNA? Could you post the bp_step.par file for the problematic structure?
Thanks,
Xiang-Jun
ry54451:
I'm using ubuntu 16.04 LTS
Attached is the x.par file I used.
Here's what I've done:
$ x3dna_utils cp_std BDNA
$ emDNA_parser --x3DNA-bp-step-params-input=x.par --get-x3DNA-bp>x.dat
> took reference frame .dat file and copied the first base pair as the new last base pair (done for circular DNA)
$ emDNA_parser --x3DNA-bp-input=x.dat --get-x3DNA-params>x_new.par
> took new par file and changed the header for a circle (first line changed value to 1014 [# base pairs for the circle], second line changed value to 0)
$ rebuild -atomic x.par x.pdb
^ it's here where I get a series of "no linkage assigned" comments due to O3' and P atom distances; for the attached .par file, I get two chain A distance comments:
1. "O3' (#10402) and P (#10415) on chain A have distance 758.5 over 4.5: no linkage assigned"
2. "O3' (#12751) and P (#12764) on chain A have distance 289.6 over 4.5: no linkage assigned"
followed by:
"xyz coordinate under f8.3 limit. reset origin to minimum xyz coordinates"
"Segmentation fault (core dumped)"
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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.