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Messages - ry54451

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A research assistant and I noticed an error upon searching for PDB IDs listed here using the "Analysis" tool on w3DNA 2.0: [6JVZ, 6JW4, 6JW3, 6JW5, 6JW0, 6JW2, 6JW1, 6JTQ, 6LEW]

Error Message: "ERROR: Empty or invalid ID, please type in a valid one."

These IDs are deposits dated either in 2019 or 2020. I did a search for 2021 deposits with DNA and did another set of 'Analysis' checks and, again, got the same error.

Is there a lag time between when a PDB deposit is made vs. when it's able to be accessed in the web server?

2
I was curious to know what resources you are using for the A-DNA, B-DNA, and C-DNA parameters when constructing examples on w3DNA. I cannot find them on the forum or the website. Thank you.

3
In this process, you generate the parameter file with two header lines.
I understand what the 1st line means.
What does the value associated with the 2nd line mean? I see that it is '0' , but why have it? What does it signify?

Thank you.

4
General discussions (Q&As) / Re: Circular DNA and Groove Information
« on: March 22, 2019, 11:40:37 am »
Well, when I get my circular reference frame files, my last frame is numbered 1 instead of N+1. My last row in my circular parameter file is the first base-pair.
So, if anything, I would suggest the following:

N-1 C-G     14.41     14.37     19.81     19.75
   N G-C     14.32     14.27     19.86     19.79
    1 A-T     14.32     14.27     19.86     19.79

5
General discussions (Q&As) / Re: Circular DNA and Groove Information
« on: March 22, 2019, 11:23:43 am »
I downloaded and checked the latest DSSR for --circular-analyze and the groove information looks great.

There is an issue with the parameter data section (both wimple and based on consecutive C1'-C1' vectors): If I have N base pairs I will have N base-pair steps for circular DNA. The output stops at the N-th base pair but there is still one step of information between the Nth-1st base pair.

Finally, at the bottom of the output file is this truncated Global Linear Helical Axis section. Was that by design as you were testing the new code or is this a bug?

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General discussions (Q&As) / Re: Circular DNA and Groove Information
« on: March 19, 2019, 10:34:39 am »
That sounds great!
It's been my experience that there doesn't need to be a new way of arranging the base pair nor the base pair step parameters except that the first base pair will need to be repeated at the end (N base pairs so N base pair steps) in order to collect the last base pair step data.

7
General discussions (Q&As) / Circular DNA and Groove Information
« on: March 08, 2019, 03:20:45 pm »
Thanks for an absolutely fantastic software package. I've been able to devote more time to understanding it while improving my own programming skills and you've done a brilliant job with 3DNA.

I wanted to know if you had any plans on incorporating circular analysis? I ask as I work with 336bp and 1014bp circles and would like to get minor-/major-groove data. However, the first and last few entries lack values. I've been looking at the cited paper to get a better idea with maybe calculating it on my own, but I wanted to know if circular analysis was on the radar.

Again, thanks for your time.

Note: I've posted a simple planar circle as an example.

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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.

9
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.

10
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?

11
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).

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*** 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)"

13
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)"


14
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.

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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?

16
Good afternoon.
I'm needing to generate ref_frame and/or .par files from a series of pdb files sent to me by a collaborator. These pdb files are from MD work (from 'ptraj'). Upon inspection of the pdb file, they lack CONECT information at the bottom and the final letter code column on the far right.

However, I have been able to generate my desired files from most of these pdb files. There are a few, however, that the number of base pairs and the number of bases do not match. I'm expecting 336 base pairs and I only get data for 335, 334, or 332. PYMOL use shows that these trajectories do not have base pairing, some bases ninety-degrees from its complement. However, my 3DNA files do not give me 672 base info, only 335*2, 334*2, or 332*2.

Here's my question: Is there a way using 3DNA that even if the bases are not bound, I should get values for them so that every 'find_pair' and 'analyze' output file is made up of 336*2 bases? I've attached two files in particular that are of frustration.

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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.