Recent Posts

1

General discussions (Q&As) / Re: Generation of ssDNA PDB with m3C modification using 3DNA webserver

« Last post by xiangjun on February 28, 2025, 08:47:06 am »

Welcome back.

But I do not have a PDB structure with the m3C modification, I was hoping that we would be able to generate the PDB (and PSF) using 3DNA/DSSR by specifying the residues.

Are you expecting 3DNA/DSSR to "generate the PDB" by specifying the residues, including unknown ones?  3DNA/DSSR can build DNA/RNA structures with standard bases (A,C,G,T,U), or modified ones with *known* building block as illustrated in 5-methylcytosine in the FAQ. It does not generate structures for ligands like m3C. It is up to the user to provide such building blocks for 3DNA/DSSR to proceed. CCP4 and Phenix may have utilities to generate new ligands.

By the way, what does PSF stand for?

As a side question, what would be a good force field that can allow us to perform a phase separation simulation with the methylated ssDNA and IDR sequence?

Sorry, I'm not familiar with this field, and I cannot offer any valuable suggestions. Overall, this question is out of the scope of the Forum.

Best regards,

Xiang-Jun

2

General discussions (Q&As) / Re: Generation of ssDNA PDB with m3C modification using 3DNA webserver

« Last post by Sunera on February 27, 2025, 11:24:32 pm »

Hi Dr. Jun,

Sorry for the late reply. Yes, I definitely think the idea in the FAQ is relevant. But I do not have a PDB structure with the m3C modification, I was hoping that we would be able to generate the PDB (and PSF) using 3DNA/DSSR by specifying the residues.

As a side question, what would be a good force field that can allow us to perform a phase separation simulation with the methylated ssDNA and IDR sequence?

3

MD simulations / Re: Update of do_x3dna package

« Last post by xiangjun on February 22, 2025, 11:23:27 pm »

Hi Rajendra,

Thanks for the update to do_x3dna for GROMACS-2025. It is great that the "binary package can be used with files generated by any version of GROMACS". Over the years, I've received emails about applying 3DNA to MD simulations, and I know that your do_x3dna package is well received by the community.

Best regards,

Xiang-Jun

4

MD simulations / Update of do_x3dna package

« Last post by rkumar on February 22, 2025, 11:12:53 pm »

Dear All,

I have updated the do_x3dna package for GROMACS-2025. I have built binary executable of do_x3dna that can be downloaded and used without any compilation. Most importantly, this binary package can be used with files generated by any version of GROMACS.

Thanks,
Dr. Rajendra Kumar
Associate Professor
NIPER, Mohali, India

5

General discussions (Q&As) / Re: Opening values and the definition for base-pair parameters

« Last post by xiangjun on February 07, 2025, 10:22:26 am »

Hi Jing,

Please follow what I suggested in the previous response. As for the 3DNA source code, did you notice the download link at the top and the Download instructions post?

Best regards,

Xiang-Jun

6

General discussions (Q&As) / Re: Opening values and the definition for base-pair parameters

« Last post by azurelegend on February 06, 2025, 09:23:25 pm »

Hi Xiang-Jun,

Thank you so much! I'll take time to explore on it. By the way, last time you said the 3DNA source code is available, where could I find it?

Best,
Jing

7

General discussions (Q&As) / Re: Opening values and the definition for base-pair parameters

« Last post by xiangjun on February 06, 2025, 11:14:10 am »

Hi Jing,

I have attached several pictures here. They are G and G pairs. The first two are with the opening \~180, the third picture is with \~-180, and the last two are with \~90.

Thanks for your follow up, and for providing images that illustrate G.G pairs with opening around 180 and 90 degrees. It would have been more helpful if you attached the corresponding PDB files. When posting questions in the future, thinks about providing (mininal) examples so others can *reproduce* the cases.

Now I understand the question you're asking. Let's use a G+G pair in G-tetrad of G-quadruplexes as an example, which has an opening around 90 degrees. Assuming you have downloaded the coordinates file `5ua3.pdb` for PDB entry 5ua3 on "Crystal structure of a DNA G-quadruplex with a cytosine bulge". Please try the following DSSR commands:

Code: [Select]

# This extract DG1 and DG6 from chain A into file 5ua3-GG.pdb
x3dna-dssr -i=5ua3.pdb --select-residue='A 1+6' -o=5ua3-GG.pdb

# Set the pair into the base reference frame of A.DG1
x3dna-dssr -i=5ua3-GG.pdb --frame='A.1' -o=5ua3-GG-frame1.pdb

# Generate the schematic with base blocks
x3dna-dssr -i=5ua3-GG-frame1.pdb --cartoon-block=sticks-label --block-file=slim-outline -o=5ua3-GG-frame1.pml
Load `5ua3-GG-frame1.pml` into PyMOL to see the attached image where the (`slim`) base blocks are nearly perpendicular, corresponding to an opening angle of ~90 degrees.

Analyze `5ua3-GG.pdb` (or `5ua3-GG-frame1.pdb`) with `--more` option to see the six base-pair parameters, including opening.

Code: [Select]

x3dna-dssr -i=5ua3-GG.pdb --more

# With the following detailed information:
List of 1 base pair
     nt1            nt2            bp  name        Saenger   LW   DSSR
   1 A.DG1          A.DG6          G+G --          06-VI     cWH  cW+M
       [-131.0(anti) ~C2'-endo lambda=62.6] [-128.4(anti) ~C2'-endo lambda=28.0]
       d(C1'-C1')=11.59 d(N1-N9)=9.65 d(C6-C8)=9.30 tor(C1'-N1-N9-C1')=10.9
       H-bonds[2]: "N1(imino)-O6(carbonyl)[2.95],N2(amino)-N7[2.91]"
       interBase-angle=1  Simple-bpParams: Shear=-2.67 Stretch=2.83 Buckle=-0.8 Propeller=0.5
       bp-pars: [1.61    3.54    -0.15   0.14    0.94    -89.63]
Note that the opening is reported as `-89.63` --- if you try to align A.DG6 to A.DG1, you need to rotate ~`-90` degrees as can be seen in the attached images. If you swap the pair, the opening would be ~`+90` degrees. See the [2003 3DNA paper in NAR](https://doi.org/10.1093/nar/gkg680), specifically the section "Base pair parameters".

With a clear understand of the above example, you should have little difficult in understanding opening ~180 degrees. You are suggested to follow the above example on one of such cases, and report back your findings.

Note that 3DNA/DSSR report angular parameters in the range of [0, +-180] instead of [0, 360]. So opening of `-175` is not that much a difference from `+175` (vs `+185`). Also notice the opposite sign of opening for M+N vs N+M pairs.

Please read the [DSSR manual](http://docs.x3dna.org/dssr-manual.pdf) and the [practical guide for the DSSR-PyMOL](http://skmatic.x3dna.org/dssr-schematic-guide.pdf) article.

Best regards,

Xiang-Jun

8

General discussions (Q&As) / Re: Opening values and the definition for base-pair parameters

« Last post by azurelegend on February 06, 2025, 12:45:48 am »

Hi Xiang-Jun,

Thanks for replying! I have attached several pictures here. They are G and G pairs. The first two are with the opening ~180, the third picture is with ~-180, and the last two are with ~90.

Best,
Jing

9

General discussions (Q&As) / Re: Opening values and the definition for base-pair parameters

« Last post by xiangjun on February 03, 2025, 06:05:26 pm »

Hi Jing,

Thanks for using 3DNA, and for posting your questions on the Forum. Your confusions about the details are understandable, and can be clarified most effectively using concrete examples. Do you have examples with opening ~90 and 180?

Since 3DNA source code is available, you can dig into it to see exactly how the base reference frames are defined and how the various parameters are calculated.

Best regards,

Xiang-Jun

10

General discussions (Q&As) / Opening values and the definition for base-pair parameters

« Last post by azurelegend on February 03, 2025, 04:44:26 pm »

Hi,

I'm using X3DNA to analyze the base-pair parameters and the base step parameters recently. My structure is parallel-stranded DNA and all the base pairs are non-canonical pairs. I found that some parameters are very different from a standard DNA structure. For example, the opening will have values like 170, -170, 90. I read some of the related posts and papers but still confused about the definitions. So what do the 170s and 90s value mean? And what is the difference between 170 and -170? How does X3DNA calculate the opening, that is, which angle does it actually calculate?

And I also have a further question that how does X3DNA calculate other base-pair parameters? I think I'm getting confused even from the beginning, how were the (o1, x1, y1 ,z1) and (o2, x2, y2, z2) for each base in a certain base-pair defined?

Thanks in advance,
Jing