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Messages - xiangjun

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1
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

2
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

3
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

4
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



5
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

6
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

7
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


8
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

9
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


10
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



11
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

12
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

13
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

14
Hi Cathy,

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

Xiang-Jun

15
Hi Cathy,

Thanks for your kind words about our Web 3DNA 2.0 publication in NAR. Shuxiang has done an excellent job to bring the 3DNA web server up to date and highly usable for the years to come.

I noticed that the cover images of recent issues of the RNA Journal were contributed by the NDB. The cover image and its caption of the August 2019 issue are shown below. Thanks for your generous mention of the 3DNA/blocview program!


"Crystal structure of the metY SAM V riboswitch (Protein Data Bank code: 6fz0; Huang L, Lilley DMJ. Structure and ligand binding of the SAM-V riboswitch. 2018. Nucleic Acids Res 46: 6869–6879). The RNA riboswitch backbone is displayed as a red ribbon; bases are shown as blocks with NDB coloring: A—red, C—yellow, G—green, U—cyan; the intercalating S-adenosylmethionine (SAM) ligand is shown in spacefill with element colors: C—white, N—blue, O—red, S—yellow. The image was generated using 3DNA/blocview and PyMol software. Cover image provided by the Nucleic Acid Database (ndbserver.rutgers.edu)."


Enjoy the summer!

Xiang-Jun

16
General discussions (Q&As) / Re: install xdna on linux
« on: August 04, 2019, 09:13:26 pm »
You need to add the two lines:

Code: [Select]
export X3DNA='/home/sima/x3dna-v2.4'
export PATH='/home/sima/x3dna-v2.4/bin':$PATH

into your ~/.bashrc file so that you can access 3DNA commands each time you open a new terminal window.

Or, you can place the two lines into a file, and then source that file each time you open a new terminal window.

Xiang-Jun

17
General discussions (Q&As) / Re: install xdna on linux
« on: August 04, 2019, 10:52:24 am »
In your current settings, what happens when you run: find_pair -h?

Change to the directory when 3DNA is installed, then type: pwd. What is the result?

What is the output of: echo $SHELL

Xiang-Jun

18
RNA structures (DSSR) / Re: how to define base pair and co-stacking
« on: August 01, 2019, 11:56:33 am »
Hi Chenjie,

Check the DSSR NAR'15 paper. For base-pair identification and characterization, the 3DNA NAR03 paper is still valid and relevant. You may check the 3DNA source code for details.

Best regards,

Xiang-Jun

19
RNA structures (DSSR) / Re: Noncanonical base pair standards
« on: August 01, 2019, 11:30:40 am »
Hi Mauricio,

Thanks for chiming in. With DSSR, it won't be difficult to compile a list of all types of base-pairs (bp) in the PDB (or any user-selected dataset) with corresponding bp parameters. It is important to note, however, that no one-to-one correspondence exists between the 12 LW qualitative bp classes and the far more abundant types in reality. The outdated and dysfunctional BPS database, compiled based on 3DNA results, does not contain LW classification information.

Best regards,

Xiang-Jun

20
RNA structures (DSSR) / Re: --nmr option with --get-hbond & --analyze
« on: July 27, 2019, 10:00:53 am »
Hi,

Glad to hear that the --json option with --nmr does the trick for you. I won't argue with you (or any DSSR user) about the best approach to a particular use case. Overall, though, the structured JSON output is the way to go for parsing data -- it is the USB connector between different parts (programs). In my knowledge of DSSR usages, the JSON output is indeed the preferred way to take advantage of what DSSR has to offer. For example, the DSSR-Jmol interface relies on JSON format. As a more up-to-date example, the DSSR R wrapper from "VeriNA3d: an R package for nucleic acids data mining" (https://doi.org/10.1093/bioinformatics/btz553) employes JSON output as well -- see my blogpost "R wrapper to DSSR in VeriNA3d".

The --nmr and --non-pair combination works as you expected because non-pairing interactions are part of DSSR output. The DSSR output was initially in text format only before the JSON option was introduced. The --get-hbond option, on the other hand, is auxiliary and internal to DSSR. After all, there are numerous other ways to detect H-bonds, including the dedicated tools HBPlus and HBExplore, for example. I'm glad to see the community like this 'extra' feature from DSSR, presumably due to its robust performance in real-world applications.

As a side note, the DSSR JSON output actually contains more information about H-bonds than that from the text output. I have no doubt that these features would be put into good use by the community someday.

Best regards,

Xiang-Jun

21
RNA structures (DSSR) / Re: Avoiding pairing that cross chains
« on: July 27, 2019, 09:40:06 am »
The attached, bio3d-extracted PDB file is not in the proper PDB format, as shown below:

Code: [Select]
ATOM  146941 "O5'"   U A5   1      25.028 -40.244  90.648  1.00 70.00           O
ATOM  146942 "C5'"   U A5   1      25.523 -39.579  91.790  1.00 70.00           C
ATOM  146943 "C4'"   U A5   1      26.370 -38.340  91.444  1.00 70.00           C
ATOM  146944 "O4'"   U A5   1      27.391 -38.705  90.570  1.00 70.00           O
ATOM  146945 "C3'"   U A5   1      25.628 -37.207  90.717  1.00 70.00           C
ATOM  146946 "O3'"   U A5   1      24.913 -36.404  91.694  1.00 70.00           O
Specifically, the atom serial number is larger than 99999 (maximum for 5 columns), the atom names are more than 4-chars with "", and chain id should be only one character long instead of A5. Could bio3D write the output in mmCIF format? You may need to read the documentation or contact the developer of bio3D.

An example of correctly formatted PDB ATOM record is as below:

Code: [Select]
ATOM     25  P     C A   2      54.635  50.420  53.741  1.00100.19           P
ATOM     26  OP1   C A   2      55.145  51.726  54.238  1.00100.19           O
ATOM     27  OP2   C A   2      54.465  50.204  52.269  1.00100.19           O
ATOM     28  O5'   C A   2      55.563  49.261  54.342  1.00 98.27           O
ATOM     29  C5'   C A   2      55.925  49.246  55.742  1.00 95.40           C
ATOM     30  C4'   C A   2      56.836  48.075  56.049  1.00 93.33           C
ATOM     31  O4'   C A   2      56.122  46.828  55.830  1.00 92.18           O
ATOM     32  C3'   C A   2      58.090  47.947  55.197  1.00 92.75           C
ATOM     33  O3'   C A   2      59.174  48.753  55.651  1.00 92.89           O
ATOM     34  C2'   C A   2      58.416  46.463  55.298  1.00 91.81           C

To help move over this issue quickly, please try the following in PyMOL:

Code: [Select]
reinitialize
load 4v6w.cif
save 4v6w-A5.cif, chain A5

The output file "4v6w-A5.cif" is what you need. Please have a try and let us know how it goes.

Xiang-Jun

22
RNA structures (DSSR) / Re: --nmr option with --get-hbond & --analyze
« on: July 26, 2019, 08:42:52 pm »
Hi Amir,

The H-bonding info of each frame/model of the ensemble is available via the --json option. Please have a try and report back how it goes.

Xiang-Jun

23
Hi Shuxiang,

Tdst and Rdst mean translational and rotational distances, respectively. The negative values reflect the relative position (e.g., the C-alpha atom above or below a base plane).

Xiang-Jun
 

24
RNA structures (DSSR) / Re: Avoiding pairing that cross chains
« on: July 26, 2019, 03:01:46 pm »
It really depends. There are many choices. For example, pdb-tools 2.0.0: Have a look of https://pypi.org/project/pdb-tools/ [pdb-tools: a swiss army knife for molecular structures. bioRxiv (2018). doi:10.1101/483305]. Jmol/PyMOL should also do the trick.

Best regards,

Xiang-Jun

25
RNA structures (DSSR) / Re: Avoiding pairing that cross chains
« on: July 26, 2019, 02:18:32 pm »
Dear Eric,

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

Quote
Is there a way to force pairings only within single chains (i.e., intra-chain pairs only)?

The default setting of DSSR is there for a reason. Thinking of a DNA duplex, such as 355d for an example. There would be no base pairs within each strand (A, or B). So the DSSR DBN output for the [whole] input structure is balanced, but not necessarily within each chain, as you noticed in PDB 4V6W.

To derive properly formatted DBN per chain, you need to extract the chain into a new file and then run DSSR on it. I may consider adding a new option to DSSR to streamline this process in the future.

Best regards,

Xiang-Jun

Pages: [1] 2 3 ... 55

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.