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Messages - xiangjun

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1
Quote
It worked with do_x3dna VMD plugin.

I do not know if it works now. For any do_x3dna specific questions, please ask the authors/developers directly. I was not involved in that project and I cannot provide any practical help for do_x3dna.

Best regards,

Xiang-Jun

2
Quote
I tried with the changes you suggested and it worked.

Glad to hear that the suggested method works. Thanks for the update.

Quote
Now another doubt is I have to run these calculations for multiple PDB files at a time. I guess analyze option is overwriting the file names wehn I am trying to run in for loop and I could not find any option to give the output file name after analyze command.

Since you are running 'analyze' in a loop to process multiple PDB files, you should be able to rename the default output file as desired. Without further details, that's all I could say.

Best regards,

Xiang-Jun

3
Hi Tanashreee,

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

Quote
I added the name in baselist.dat I am using 2.0 version.  Also, I kept the Atomic_TG.PDB file in config folder as shown for 5MC modification.  When I tried to analyze program is analyzing just for the 10 base pairs and not all 13.

Please upgrade to 3DNA v2.4, which detects 12 base-pairs out of the expected 13. Version 2.0 is more than 10 years old, and there is no practical reasons to use it anymore.

3DNA does not detect the ADE-TG pair due to improper labeling of base atoms in the modified TG. See the attached image of the pair, and pay close attention to the TG base ring (e.g., C7 connects to N1 etc.)

Rectify names of the TG base atoms following PDB convention (as for T), 3DNA should then work. Please have a try and report back how it goes.

Best regards,

Xiang-Jun





4
DNA/RNA-protein interactions (SNAP) / Re: About sugar-pi stacking
« on: November 08, 2019, 04:27:51 pm »
Hi Honglue,

Have you found a solution to your sugar-pi stacking task? If so, you are encouraged to share your findings with the 3DNA Forum community. If you have not found a practical solution yet and you are still interested in this topic, I may consider to add this feature to SNAP.

Best regards,

Xiang-Jun

5
DNA/RNA-protein interactions (SNAP) / Re: About sugar-pi stacking
« on: October 17, 2019, 04:55:36 pm »
Hi Honglue,

The current version of SNAP does not detect sugar-pi stacking interaction in DNA-protein complexes. Only 'classic' stacking interactions between base and planar side chains (e.g., ARG, HIS, TRP etc) are reported. This is one of the areas that would be enhanced in futures releases of SNAP.

Regarding DNA-protein interactions in general, you may want to have a look of DNAproDB from the Remo Rohs laboratory. A new paper has just been published in NAR, "DNAproDB: an expanded database and web-based tool for structural analysis of DNA–protein complexes".

For sugar-pi stacking in particular, why not ask the authors on how they detected the reported interactions? Hopefully, they may provide directly what you need.

Best regards,

Xiang-Jun

6
MD simulations / Re: Filter frayed ends or broken H bonds
« on: October 11, 2019, 08:54:11 am »
See FAQ entry: "How to fix missing (superfluous) base pairs identified by find_pair?" (http://forum.x3dna.org/faqs/how-to-fix-missing-(superfluous)-base-pairs-identified-by-find_pair/)

Again, if you provide a concrete example, we could discuss the issue in more detail.

Best regards,

Xiang-Jun

7
MD simulations / Re: Filter frayed ends or broken H bonds
« on: October 10, 2019, 09:09:46 am »
Hi Rahul,

Please use concrete examples to illustrate unambiguously what you want to achieve.

Thanks.

Xiang-Jun

8
Hi,

Thanks for providing a detailed example. It is completely fine, even preferable, to use a simplified data set just to illustrate the issue at hand.

With the data files and steps you provided, I can now understand clearly where the issue is. The 3DNA programs are working as expected, but one step is missing. Please try the following:

Code: [Select]
# Create a text file ('rot_yz180', attached), with the following content:
by rotation y 180
by rotation z 180

# transform file 'part-2_aligned.pdb' (attached), as below
rotate_mol -r=rot_yz180 part-2_aligned.pdb part-2_aligned-rotated.pdb

Now use part-2_aligned-rotated.pdb instead of part-2_aligned.pdb in your concatenated file. Have a try and report back how it goes.
 
Xiang-Jun

9
Would it be feasible that you attach all the PDB files? Without those data files, it is impossible to reproduce the reported image and it is hard (for me at least) to pinpoint exactly where the issue is.

Xiang-Jun

10
Please be specific with detailed steps you took and problems you experienced.

Thanks,

Xiang-Jun

11
RNA structures (DSSR) / Re: Wrong junctions
« on: September 30, 2019, 10:39:52 pm »
As a follow-up, I've released DSSR v1.9.7-2019oct01 that's fixed the reported issue.

Xiang-Jun

12
RNA structures (DSSR) / Re: Wrong junctions
« on: September 17, 2019, 11:44:51 pm »
Hi Jun,

I've updated DSSR (still labelled v1.9.6-2019sep16). It should have fixed the junction issue (in the first 3-way junction case) you observed in PDB entry 4wsm. See also my note on junctions with pseudoknots.

Please have a try and report back how it goes. In reporting any further issues, please remain to be specific.

Best regards,

Xiang-Jun

13
RNA structures (DSSR) / Re: Wrong junctions
« on: September 17, 2019, 04:49:28 pm »
Hi Jun

Please provide more details with the additional PDB entries, as you did for 4wsm. I believe the underlying issue is similar, most likely associated with extreme cases with distorted structures. The more detailed cases you provide, the better I can test/validate the fixes for the next DSSR release.

Best regards,

Xiang-Jun

14
RNA structures (DSSR) / Re: Wrong junctions
« on: September 17, 2019, 01:56:52 pm »
Hi Jun,

A junction loop derived by DSSR may share the same stem when pseudoknots are involved, as emphased in the DSSR paper (https://doi.org/10.1093/nar/gkv716). See for example, Figure 4 for the env22 twister ribozyme, PDB id: 4rge. Generally speaking, this is a unique feature, instead of a bug, of DSSR. Such junctions are noted with a suffix * after the serial number. One can get rid of such loops by specifying the --nested option.

I've a quick look of your reported case on 4wsm, and noticed that there may be a bug in DSSR. The first case (a three way junction) should not be there. The issue is due to stem#101 (with 2 base pairs) which has a highly distorted geometry, and judged as parallel by DSSR. I will look into the issue further, and get back to you soon.

In the meantime, you could take it as a special case, or simply remove junctions with a * suffix.

Thanks for reporting the issue!

Xiang-Jun

15
General discussions (Q&As) / Re: Different shear etc. 3 DNA and Curves+
« on: September 11, 2019, 11:04:49 am »
Quote
I have the following question. I calculated the shear, buckle etc. for a DNA dimer ( PDB 355d.pdb  same as the one in "Building a bridge between Curves+ and 3DNA") with 3DNA and with Curves+. I would have expected to get identical values for the shear, buckle roll etc. with both programs. However, that is not the case. e.g. shear for the first base pair using 3DNA is  0.28 and using Curves+ is 0.13, propeller -17.31 resp. -18.5

It is unrealistic to expect 3DNA and Curves+ to give identical values of base-pair parameters for a given structure. Even with the same Curves+ program, setting fit=.t. or not would give slightly different results. By adopting the standard base reference frame, 3DNA and Cuves+ give similar (but not identical) values for intra- or inter-base pair parameters. See the following blogposts:
Please also refer to the Web 3DNA 2.0 paper where further comparisons were made between 3DNA and Curves+.

Quote
Why is there such a difference? Is there a different convention/parameters for the calculation in 3DNA compared to Curves+?

As always, the devil is in the details. The differences between 3DNA and Curves+ come mainly from two aspects: (1) they implement the standard base reference frame differently; (2) they use different algorithms to calculate base-pair and step parameters. Since both programs are open source, you are welcome to dig into the technical details.

HTH,

Xiang-Jun



16
General discussions (Q&As) / Re: Recognition of stacked base pairs
« on: September 08, 2019, 06:54:44 pm »
As a follow-up, I've updated 3DNA to v2.4.4-2019sep09. It fixes the issue of inconsistent stacking area you experienced. Using C3GAGA_full.pdb as an example, the output for the overlap area section is as below:

     step      i1-i2        i1-j2        j1-i2        j1-j2        sum
   1 AG/GA  1.87( 0.00)  0.00( 0.00)  0.00( 0.00)  6.49( 4.35)  8.36( 4.35)
   2 GA/AG  7.03( 4.09)  0.00( 0.00)  0.00( 0.00)  6.52( 4.42) 13.55( 8.51)
   3 AG/GA  0.00( 0.00)  6.09( 4.69)  5.95( 4.04)  0.00( 0.00) 12.04( 8.73)
   4 Gc/CG  7.10( 4.01)  0.00( 0.00)  0.00( 0.00)  6.11( 3.06) 13.21( 7.07)
   5 cC/cC  0.00( 0.00)  0.00( 0.00)  4.08( 1.06)  0.00( 0.00)  4.08( 1.06)
   6 CC/cc  0.00( 0.00)  3.84( 0.77)  1.04( 0.00)  0.00( 0.00)  4.88( 0.77)
   7 Cc/Cc  0.00( 0.00)  0.00( 0.00)  2.25( 0.64)  0.33( 0.00)  2.59( 0.64)
   8 cc/CC  0.00( 0.00)  2.66( 0.10)  1.49( 0.00)  0.04( 0.00)  4.19( 0.10)
   9 cC/cC  0.08( 0.00)  0.19( 0.00)  0.63( 0.00)  0.83( 0.00)  1.72( 0.00)
  10 CG/Gc  8.08( 4.05)  0.00( 0.00)  0.00( 0.00)  4.96( 2.33) 13.04( 6.38)
  11 GA/AG  0.00( 0.00)  5.76( 3.86)  6.23( 4.66)  0.00( 0.00) 12.00( 8.52)
  12 AG/GA  5.89( 3.84)  0.00( 0.00)  0.00( 0.00)  4.70( 2.58) 10.59( 6.42)
  13 GA/AG  5.59( 2.76)  0.00( 0.00)  0.00( 0.00)  3.24( 0.73)  8.83( 3.49)


Best regards,

Xiang-Jun

17
General discussions (Q&As) / Re: Recognition of stacked base pairs
« on: September 08, 2019, 03:21:28 pm »
Hi,

Thanks for bringing up an insightful case of inconsistent characterization of base-stacking interactions in 3DNA v2.x. The details you provided are reproducible and helped me to detect where the problem is.

Quote
1) Is there any explanation why the overlap area in the G4-A5 step in the full structure is zero but in extracted structure is 12.04?
2) Is it possible that zero overlap is result of low threshold?
3) If so, is it possible to change the threshold and how?

The inconsistency is due to the different arrangement bases along the two chains. For C3GAGA_full_analyze.out, it is as below:
            Strand I                    Strand II          Helix
   1   (0.073) ....>A:...7_:[.DA]A-**+-A[.DA]:..21_:C<.... (0.065)     |
   2   (0.087) ....>A:...6_:[.DG]G-**+-G[.DG]:..20_:C<.... (0.071)     |
   3   (0.060) ....>A:...5_:[.DA]A-**+-A[.DA]:..19_:C<.... (0.069)     |
   4   (0.061) ....>A:...4_:[.DG]G-**+-G[.DG]:..18_:C<.... (0.072)     |
   5   (0.060) ....>A:...3_:[HCY]C-**+-C[.DC]:..17_:C<.... (0.049)     |

For G4A5_analyze.out, the bases are swapped, as shown below:
            Strand I                    Strand II          Helix
   1   (0.069) ...3>C:..19_:[.DA]A-**+-A[.DA]:...5_:A<...3 (0.060)     |
   2   (0.061) ...3>A:...4_:[.DG]G-**+-G[.DG]:..18_:C<...3 (0.072)     |

It turns out that this rearrangement is consequential in your case. If you're interested in knowing the technical details, please check the source code; particularly, the two functions with_stacking() and with_ss_overlap() in file ana_fncs.c.

You may give DSSR a try. With the --non-pair option, you'd get a consistent result for the overlap area of any two stacked bases. For example, run the command x3dna-dssr -i=C3GAGA_full.pdb --non-pair, you'd see the following:

Code: [Select]
List of 27 non-pairing interactions
.....
   6 A.DG4   C.DA19  stacking: 6.3(4.7)--pm(>>,forward) interBase-angle=1 min_baseDist=3.46
   7 A.DA5   A.DG6   stacking: 6.5(3.8)--pm(>>,forward) interBase-angle=15 connected min_baseDist=3.08
   8 A.DA5   C.DG18  stacking: 6.1(4.7)--mp(<<,backward) interBase-angle=7 H-bonds[1]: "O4'-N1(imino)[3.20]" min_baseDist=3.23
   9 A.DG6   A.DA7   stacking: 2.4(0.0)--pm(>>,forward) interBase-angle=7 connected min_baseDist=3.55
......

With the --analyze option, you can also get base-pair parameters as from 3DNA v2.x analyze program.

HTH,

Xiang-Jun

18
RNA structures (DSSR) / Re: DSSR of 32 bit version
« on: August 28, 2019, 12:37:44 pm »
Hi Jun,

Glad to hear that the Linux 32-bit version of DSSR is working.

I heard Dr. Shi-Jie Chen talking about 3DSSR at a workshop last year. I am delighted to know that DSSR and 3DSSR are now connected.

Best regards,

Xiang-Jun


19
RNA structures (DSSR) / Re: DSSR of 32 bit version
« on: August 28, 2019, 11:51:13 am »
Hi Jun,

Thanks for your feedback. I've compiled DSSR (and SNAP) on Ubuntu 16.04 Linux 32-bit, which is available in the normal registration-only download page. Have a try and let me know how it goes.

It is a pleasure to know DSSR is being integrating into your server. Is it convenient to share with us now what your server is about? Some viewers of the Forum may be interested in your work.

Best regards,

Xiang-Jun

20
RNA structures (DSSR) / Re: Stacking parameters (again)
« on: August 27, 2019, 10:31:45 pm »
Dear Simón Poblete,

Thanks for coming back. My response in the initial thread on "Stacking parameters" still holds. The basic idea for defining two bases as stacked has been reported in the 2003 3DNA NAR paper and the 2015 DSSR paper. If you want to dig into details, check the 3DNA source code.

If you could elaborate specifically on what to you want to extract from DSSR for base-stacking interactions, I may be able to offer more concrete help.

Best regards,

Xiang-Jun


21
RNA structures (DSSR) / Re: DSSR of 32 bit version
« on: August 27, 2019, 10:20:24 pm »
Hi Jun,

I am curious about the nature of the DSSR 32-bit issue you experienced.

In the thread "Stems of junction structure have only one base pair" you initiated on January 15, 2019, you wrote:

Quote
I am using the newest DSSR to extract the junction structure, but the stems of some junctions have only one base pair...

Do you remember which version of DSSR you used at that time?

In the current thread, you noted that "The DSSR of the latest version cannot be used on 32 bit OS". What DSSR version is this one?

As far as I can remember, the distributed DSSR versions since 2018 have all been of 64-bit for Linux. I am wondering how could you be able to run DSSR in January but not in August? Did you switch a Linux distribution from 64-bit to a 32-bit?

How difficult is it for you to install a Linux 64-bit distribution? It seems to me that Linux 32-bit OS is out of fashion. Indeed, your request for a DSSR version on Linux 32-bit is the first for over one year since 2018.

I used to have access to a Linux 32-bit OS via an external resource. Unfortunately, it is no longer available. If upgrading your Linux to 64-bit is not an option, I will consider installing a local Linux 32-bit OS just to compile DSSR/SNAP for use cases like yours.

Xiang-Jun



22
RNA structures (DSSR) / Re: DSSR of 32 bit version
« on: August 27, 2019, 05:21:23 pm »
Quote
32 bit OS

Which OS are you referring to, Windows, Linux, or macOS?

Xiang-Jun

23
General discussions (Q&As) / Re: create RNA sequence syn nucleosides
« on: August 09, 2019, 08:53:09 pm »
Unfortunately, the answer is no within 3DNA. Nevertheless, you may use the 3DNA fiber program to generate a structure in the anti-anti form as a starting point. There exist interactive tools (e.g., PyMOL) to rotate the desired base by its glycosidic bond into the syn form.

Xiang-Jun

24
w3DNA -- web interface to 3DNA / Re: w3dna server update schedule?
« on: August 08, 2019, 12:28:47 pm »
Hi Cathy,

Good catch!

It is in the to-do list to automatically handle newer PDB entries than the initially processed dataset dated March 6, 2019 (reported in the Web 3DNA 2.0 paper). I chatted with Shuxiang about this feature a while ago. Hopefully, the server will be updated in the near future with the functionality.

Best regards,

Xiang-Jun

25
Hi Cathy,

That's really great -- thanks for sharing the info!

Xiang-Jun

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.