Topics

1

w3DNA -- web interface to 3DNA / Is there a time lag between PDB deposits and 'Analysis' use?

« on: April 16, 2021, 10:16:42 am »

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

w3DNA -- web interface to 3DNA / Standard Values for A-, B-, C-DNA on w3DNA

« on: April 22, 2020, 06:11:47 pm »

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

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.

4

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

« on: November 06, 2018, 02:02:15 pm »

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?

5

General discussions (Q&As) / 'find_pair' and 'analyze' with pdb files of unbound base pairs

« on: April 23, 2018, 05:31:27 pm »

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.