'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)"

[ry54451]

*** CORRECTION TO CODE ****

$ 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 -at x_new.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)"

[xiangjun]

Thanks for your follow-up. Could you please install the 3DNA v2.3.4-2018nov06 so we are playing with the same version? Here are my results using the 64-bit Linux version, with the structure004.pdb file you emailed me. In my hand, 3DNA works as expected.

x3dna@tstx [2035] find_pair structure004.pdb | analyze

handling file <structure004.pdb>

Time used: 00:00:00:01
This structure has broken O3' to P[i+1] linkages

Time used: 00:00:00:03
x3dna@tstx [2036] x3dna_utils cp_std BDNA
x3dna@tstx [2037] rebuild -atomic bp_step.par 3dna-str04.pdb
xyz coordinate under f8.3 limit. reset origin to minimum xyz coordinates

Time used: 00:00:00:01

The bp_step.par and an image of 3dna-str04.pdb are attached.

Please repeat the commands above and post back your results.

Xiang-Jun

[ry54451]

Sorry for the long response time. I was running an optimization.

I think I properly updated the x3DNA software package. Starting from the .par file I sent you and not from the starting .pdb file (due to sequence), I'm still getting the same error (images 1 and 2 attached).

[xiangjun]

Please follow the instructions to help me identify where the problem is.

I got confused by your two posts dated Nov. 8. For one thing, the attached file is named tbru_mc004.par, whilst in your posts, the parameter file is called "x.par" and "new.par". What is emDNA_parser, and how is it relevant the issue at hand? The sequence in the parameter should not affect how "rebuild" runs.

Xiang-Jun

[ry54451]

My apologies about emDNA. We have a program through emDNA called parser that takes a .par file and converts it into a reference frame file, and vice-versa.

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.

However, is there a way to generate a reference frame file from a starting .par file using x3dna?

[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.

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.

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.
 

However, is there a way to generate a reference frame file from a starting .par file using x3dna?

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