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1

General discussions (Q&As) / Re: 'rebuild' and the f8.3 limit, 1014 bp circular structure

« Last post by xiangjun on November 12, 2018, 05:27:39 pm »

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

2

General discussions (Q&As) / Re: 'rebuild' and the f8.3 limit, 1014 bp circular structure

« Last post by ry54451 on November 12, 2018, 04:37:20 pm »

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.

3

General discussions (Q&As) / Re: 'rebuild' and the f8.3 limit, 1014 bp circular structure

« Last post by ry54451 on November 12, 2018, 04:12:13 pm »

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?

4

General discussions (Q&As) / Re: 'rebuild' and the f8.3 limit, 1014 bp circular structure

« Last post by xiangjun on November 12, 2018, 01:58:13 pm »

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

5

General discussions (Q&As) / Re: 'rebuild' and the f8.3 limit, 1014 bp circular structure

« Last post by ry54451 on November 12, 2018, 11:44:19 am »

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).

6

General discussions (Q&As) / Re: 'rebuild' and the f8.3 limit, 1014 bp circular structure

« Last post by xiangjun on November 08, 2018, 01:12:17 pm »

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

7

General discussions (Q&As) / Re: 'rebuild' and the f8.3 limit, 1014 bp circular structure

« Last post by ry54451 on November 08, 2018, 12:28:44 pm »

*** 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)"

8

General discussions (Q&As) / Re: 'rebuild' and the f8.3 limit, 1014 bp circular structure

« Last post by ry54451 on November 08, 2018, 12:27:28 pm »

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)"

9

General discussions (Q&As) / Re: do_x3dna not working

« Last post by Sunipa Sarkar on November 07, 2018, 10:09:15 am »

Hello Xiang
I have solved the problem by contacting Mr. Rajendra kumar. It was a problem of  PBC correction of my trajectory.
Thank you for the suggestion.

10

General discussions (Q&As) / Re: do_x3dna not working

« Last post by Sunipa Sarkar on November 07, 2018, 04:13:05 am »

Hello
Thank you for your suggestion. I am using a linux machine and trying to install the software there. Sorry I have not mentioned in the previous post. Actually I am trying to ensure whether the error is coming because of the 3DNA package installation or do_x3dna installation. Becuase I can access both the softwares. But when I am trying to analyze a trajectory file then this fatal error is coming. Should I install bothe the softwares in same path? I have install both the softwares in different paths and I have modified my bashrc file according to that.
.bashrc file:

export X3DNA='/home/prashant/software/x3dna-v2.3'
export PATH='/home/prashant/software/x3dna-v2.3/bin':$PATH
export PATH=$PATH:$X3DNA/bin
export do_x3dna='/usr/local/do_x3dna'
export PATH='/usr/local/do_x3dna/bin':$PATH

Please correct me. If this a problem regarding do_x3dna installation then I will contact Mr. Rajendra Kumar.
Thanks