Recent Posts

21

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

« Last post by xiangjun on January 31, 2025, 08:51:31 am »

Hi Sunera,

Thanks for your follow up. Is the idea in FAQ "How can I mutate cytosine to 5-methylcytosine?" relevant? Do you have a PDB structure with m3C modification?

Best regards,

Xiang-Jun

22

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

« Last post by Sunera on January 30, 2025, 06:38:05 pm »

Hello Dr. Jun,

Thank you so much for your reply. So, my intention is to conduct an all-atom intrinsically disordered protein - ssDNA phase separation simulation using the OpenMM MD suite. I was wondering how to generate the PDB for a custom DNA sequence that contains the (m3C) modification on one of the bases.

Best,
Sunera

23

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

« Last post by xiangjun on January 30, 2025, 11:10:45 am »

Hi,

Thanks for your interesting in using 3DNA and for posting your questions on the Forum.

The http://web.x3dna.org has features to build regular fiber models or customized structures (including single-stranded structure as detailed in the supplemental PDF). However, the web-server does not allow you to generate  single-stranded DNA containing a 3-methylated cytosine. The web server simply does not have 'knowledge' of what a 3-methylated cytosine is. I know of no other tools that can do this automatically.

However, 3DNA/DSSR has features that would allow for such modeling from the command line. I need more details of exactly what you want to achieve to be of further help.

See the FAQ: How can I mutate cytosine to 5-methylcytosine?

Best regards,

Xiang-Jun

24

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

« Last post by Sunera on January 30, 2025, 12:51:31 am »

Is it possible to generate a PDB of a single stranded DNA containing a 3-methylated cytosine using the 3DNA Web Server? Could you please advise on the best way to generate an all-atom PDB containing this modification if it cannot be generated using 3DNA?

25

MD simulations / Re: overwritten output files

« Last post by xiangjun on January 13, 2025, 10:47:57 am »

Hi Mamta,

The output file name is derived from the input PDB filename, by deleting extension and add ".out". Since your PDB frame is named "output-filename.pdb.${i}", the output file will always be "output-filename.pdb.out" by replacing ".{i}" with ".out". You could name your PDB frame "output-${i}.pdb" and the corresponding output file will be "output-${i}.out".

Have a look of the C source code, and the x3dna_ensemble script (x3dna_ensemble analyze -h). Overall, the x3dna-v2.4 support for MD analysis is limited. There is also do_x3dna -- I'm not sure if it is still actively maintained.

I'm in the process of incorporating x3dna-v2.4 features into DSSR (Free academic license available from CTV). Further improvement for MD support will be implemented in DSSR.

Best regards,

Xiang-Jun

26

MD simulations / Re: overwritten output files

« Last post by Mamta on January 13, 2025, 10:00:17 am »

Hi Xian- Jung,
thanks for your quick response.
I use the simple script of 3dna -
 for i in $(seq 1 3700); do
    find_pair output-filename.pdb.${i} frame${i}.bps
    analyze frame${i}.bps
done

Thanks
Mamta

27

MD simulations / Re: overwritten output files

« Last post by xiangjun on January 13, 2025, 08:30:07 am »

Hi Mamta,

Thanks for using 3DNA/DSSR and for posting your question on the 3DNA Forum. Could you please be specific with the command you used? The x3dna-v2.4 suite comes with a Ruby script 'x3dna_ensemble' for analyzing MODEL/ENDMDL delineated ensemble of NMR or MD structures. The x3dna-dssr program has an --nmr (--md) option that streamline the analysis of such ensembles.

Best regards,

Xiang-Jun

28

MD simulations / overwritten output files

« Last post by Mamta on January 13, 2025, 04:52:30 am »

Dear all,
I am analyzing the helical parameters of DNA using 3700 frames from my MD simulation, with each frame having a corresponding `.bps` file. When using a `for` loop with the `analyze` command, the output is being overwritten instead of being saved in separate files for each frame.I am using x3dna-v2.4 version. Is it possible to configure the program so that it records the data for all frames without overwriting the output?                                                                                                              Thanks for your help!
Mamta

29

RNA structures (DSSR) / Re: DNA bend angle

« Last post by xiangjun on December 30, 2024, 10:49:36 pm »

Hi Narendra,

Thanks for using DSSR and for posting your question on the 3DNA Forum. Regarding DNA bending angle in 3DNA/DSSR, please refer to the FAQ How to calculate DNA bending angle?. With DSSR, the helical axis info is available with the --more option. See the step-by-step procedures for reproducing Figure 2 -- analysis of the yeast phenylalanine tRNA (1ehz) of the 2015 DSSR paper in NAR.

For your specific example of 1fjl, DSSR readily identifies a helix (stem) with details on the helical axis. However, DSSR does not directly provide you a bending angle for reason given in the above mentioned FAQ.

Best regards,

Xiang-Jun

30

RNA structures (DSSR) / DNA bend angle

« Last post by narayana on December 30, 2024, 09:18:28 pm »

Dear Dr. Lu,

Is there a way to compute bending angle using DSSR program. From your manual I do note that it is possible, but I am not sure how I can specify to do this. For example, for 1fjl, what would be the command line instructions? Your suggestion is much appreciated.

Thank you.

Narendra