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Messages - xiangjun

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1
General discussions (Q&As) / Re: building circular DNA
« on: July 16, 2019, 12:06:01 pm »
I understood that you have been "trying to create a DNA ring system". 3DNA does not have a direct solution to this problem, neither will it likely in the general sense.

You may give NAB a try. If you find a way, please post back so other viewers may benefit.

Best regards,

Xiang-Jun
 

2
Feature requests / MOVED: building circular DNA
« on: July 16, 2019, 11:56:46 am »

3
General discussions (Q&As) / Re: building circular DNA
« on: July 15, 2019, 09:36:33 pm »
Hi,

I'm not sure I fully understand your question in a practical sense. Please be specific.

The 3DNA rebuild can generate any structure (at the base-pair level) with a set of prescribed base-pair and step parameters. It's really up to the user to build what they want.

Best regards,

Xiang-Jun
 

4
RNA structures (DSSR) / Re: strange exception
« on: July 08, 2019, 02:21:16 pm »
Quote
It seems the new version (Jul8) works very well for all my trajectory for now.

Glad to hear that the updated version works. I've just released DSSR v1.9.4-2019jul08.

Quote
By the way I am benchmarking your new version using a ribosomal structure (PDB 1FFK).
Here I attached the output using version 2017jan22 (x3dna-dssr-old) and 2019jul08 (x3dna-dssr).

Here is the output:
...
For example, it seems the new version detect less base pairs, less multiplets, is that because you adjust the criteria for base pair or something?

If you think this post should be in a separate topic, could you please help move it to a proper place?

DSSR has been under continuous development and delivery. I maintain an extensive test set that includes all known buggy cases (such as your attached examples in this thread). For each release, I test DSSR against all nucleic-acid structures in the PDB to ensure that it does not crash. Except for boundary cases, DSSR is stable from version 1.0 and backward compatible, especially with the JSON output. I am confident that DSSR is a solid software product, with robust performances in real-world applications.

If you are interested in knowing the details between the two versions you tested, please start a new thread. Please provide concrete examples (base pairs, multiplets, etc.) where the differences really bother you.

Best regards,

Xiang-Jun


5
RNA structures (DSSR) / Re: strange exception
« on: July 05, 2019, 03:25:52 pm »
Yes, I updated DSSR today. The previous DSSR version you're using should work: the "Uncaught exception 'Assertion failed'" message you reported earlier should be gone. Nevertheless, it is preferable to restart with the latest version.

Best regards,

Xiang-Jun

6
RNA structures (DSSR) / Re: strange exception
« on: July 05, 2019, 01:33:50 pm »
Hi Honglue,

I've further refined DSSR for handling special cases of loops, as in your cases. Please see an image of a fragment from your S_000020_289.pdb file. The 4-nt fragment has the following features:
  • The U6pA7 dinucleotide is on one side and the A19pU20 dinucleotide on the other
  • U6–A19 and A7–U20 form two Watson-Crick pairs
  • U6+A7 is a dinucleotide platform
  • Moreover, the four nts are co-planar, forming a tetrad (multiplet)
Is such an unusual arrangement expected?

Anyway, I believe the updated DSSR has solved all known issues. Please have a try and report back how it goes in your hand.

Best regards,

Xiang-Jun

7
RNA structures (DSSR) / Re: strange exception
« on: July 04, 2019, 09:09:26 am »
Hi Honglue,

Happy The Fourth of July Holiday!

Please try the updated DSSR on the download page, and report back how it goes. I'll delay the next DSSR release until all known issues have been resolved.

Best regards,

Xiang-Jun

8
General discussions (Q&As) / Re: locked nucleic acids/fiber
« on: July 03, 2019, 03:01:01 pm »
Glad to hear that the 3DNA-command script helped in your case.

If you have further questions that are broadly related to 3DNA (or DSSR and SNAP), please do not hesitate to ask on the Forum. In asking questions, please be as specific as possible so others can reproduce the issue. It also helps that a follow-up summary post is provided by the initiator of the thread.

Best regards,

Xiang-Jun

9
RNA structures (DSSR) / Re: strange exception
« on: July 03, 2019, 12:53:17 pm »
Check: http://forum.x3dna.org/rna-structures/dssr-release-history/

Overall, a newer version of DSSR can safely replace previous ones.

Xiang-Jun

10
RNA structures (DSSR) / Re: strange exception
« on: July 03, 2019, 11:28:16 am »
Hi Honglue,

Thanks for your follow-ups. These examples illustrate an intriguing situation in the identification of loops. Such cases never show up in the nucleic-acid-containing structures in the PDB. The DSSR source code is defensive with such special cases with an assert(), and that's what the error message is about.

Now that I have these examples to check against, it should be possible to devise a solution to all such cases. Stay tuned.

Best regards,

Xiang-Jun

11
General discussions (Q&As) / Re: locked nucleic acids/fiber
« on: July 03, 2019, 11:14:23 am »
Thanks for providing the following two crucial clarifications:

  • So "7AL" has a sugar attached to N7 (instead of N9). The attached PDB file makes it unambiguous.
  • You want to 'make a double stranded RNA which in one strand "A" would be replaced by 7AL'.

With these details, I'd say that 3DNA cannot fit your direct needs completely. You may well want to try other advanced software tools with an interactive interface (e.g., Maestro from Schrödinger). Nevertheless, the following steps may help you in the right direction. If you still want to give DSSR a try, please proceed as suggested and report back your results.

Code: Bash
  1. # set 7AL in the standard base reference frame, assuming N9--C1' connection
  2. std_base -A -fit 7AL.pdb 7AL-ref-fit.pdb
  3. # rotated the above '7AL-ref-fit.pdb' file by y-axis of 180 degrees because of N7--C1' linkage
  4. echo 'by rotation y 180' > roty180
  5. rotate_mol -r=roty180 7AL-ref-fit.pdb 7AL-refOK-fit.pdb
  6. # generate the duplex RNA fiber model with proper sequence
  7. fiber -rna -seq=UCAGACAGU RNA-fiber.pdb
  8. # get the file with base reference frames in 'ref_frames.dat'
  9. find_pair -s RNA-fiber.pdb temp.txt
  10. # reorient the above fiber model in the reference frame of A5
  11. frame_mol -5 ref_frames.dat RNA-fiber.pdb RNA-fiber-ref5.pdb
  12. # load 7AL-refOK-fit.pdb and RNA-fiber-ref5.pdb into PyMOL

HTH,

Xiang-Jun

12
General discussions (Q&As) / Re: How does 3DNA calculate rise
« on: July 03, 2019, 10:37:57 am »
Quote
I found this definition regarding rise in the Calladine 1995 JMB paper:

Rise, Dz , is simply the component along the global
helix axis of the vector joining the mid points of
successive C6-C8 lines.

I was puzzled by your above finding of 'Rise definition' in the Calladine 1995 JMB paper, titled The Assessment of the Geometry of Dinucleotide Steps in Double-Helical DNA; a New Local Calculation Scheme". Checking carefully, I noticed that the above citation comes from the "Appendix: NEWHELIX Definitions" (p.662) which uses a global helical axis, as further described below:

Quote
The expressions for Rise and Twist are clearly defined in a global sense, and they therefore depend on the overall conformation of an oligomer. Thus while these expressions are probably valid for, say, B-DNA oligomers where all base-pairs are nearly perpendicular to the overall fitted helix axis, they may not be appropriate for the analysis of other oligomers such as those that adopt the ‘‘A’’ form. It should be noted that since the magnitude of Helical Twist is in general substantially greater than the inclination of the base-pairs to the average best-fit helix-axis, the NH-values for Helical Twist are unlikely to be very different from those given by CEHS.

The CEHS definition of translational parameters (Shift-Dx, Slide-Dy, and Rize-Dz) comes on p.654:

Quote
The displacements: Dx, Dy and Dz can now be obtained by resolving the vector joining the origins of the two original base-pair triads into components along the axes of the mid-step triad.

Yes, that's the definition used in 3DNA as well.

HTH,

Xiang-Jun

13
General discussions (Q&As) / Re: locked nucleic acids/fiber
« on: July 02, 2019, 06:17:00 pm »
What 7AL looks like? Please attach an example PDB file. Do you want to create a single-stranded RNA structure with sequence UCAGaCAGU ('a' for 7AL), right? If so, then please use the 3DNA 'fiber' program to generate a canonical RNA model. We can start from there.

As a general note, it is always helpful to be concrete, and provide as much info as possible. Guessing usually does not help much.

Xiang-Jun

14
General discussions (Q&As) / Re: locked nucleic acids/fiber
« on: July 02, 2019, 05:16:53 pm »
Hi Amir,

It is possible as you suggested, although there are other ways using 3DNA. I may be able to help if you're specific on what you want to achieve.

Best regards,

Xiang-Jun

15
RNA structures (DSSR) / Re: strange exception
« on: July 02, 2019, 01:09:34 pm »
That confusion is understandable, and that's why I told you explicitly here. Ordinary users won't be bothered by the version "issue" at all.

Xiang-Jun

16
RNA structures (DSSR) / Re: strange exception
« on: July 02, 2019, 01:03:51 pm »
Yes, just download and run x3dna-dssr -v to verify. Did not you download the previous DSSR update this way?

Xiang-Jun

17
RNA structures (DSSR) / Re: strange exception
« on: July 02, 2019, 12:58:57 pm »
It is already there in the download page and the new version will be made explicit on July 4. I may revise DSSR before the formal release note, though.

Xiang-Jun

18
RNA structures (DSSR) / Re: strange exception
« on: July 02, 2019, 12:50:54 pm »
Hi Honglue,

I've further polished the DSSR code, which will be released as v1.9.4-2019jul04. I am checking the new version against all nucleic-acid structures in the PDB to ensure it works as expected.

Please use the latest DSSR (v1.9.4-2019jul04) on the download page for tests on your trajectory, and report back any issues you may encounter.

Best regards,

Xiang-Jun

19
It is a great pleasure to see that our article "Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures" has been highlighted in the cover page of the web server issue of NAR’19. According to the editor, This year, 331 proposals were submitted and 122, or 37%, were approved for manuscript submission. Of those approved, 94, or 77%, were ultimately accepted for publication. Overall, that corresponds to a ~28% acceptance rate.

The cover image and its caption are shown below. Moreover, details on how the cover image was created are available on the 3DNA Forum.

Caption: Examples of customized molecular models that can be generated with 3DNA: (top) a chromatin-like, nucleosome-decorated DNA with the structures of known histone-DNA assemblies placed at user-defined binding sites; (lower left) molecular schematic of a DNA trinucleotide diphosphate illustrating the base planes and reference frames used to construct and analyze 3D nucleic acid-containing structures; (lower right) customized single-stranded tRNA model built from a user-defined base sequence and a set of rigid-body parameters describing the desired placement of successive bases. Color code of base blocks: A, red; C, yellow; G, green; T, blue; U, cyan.

20
RNA structures (DSSR) / Re: strange exception
« on: July 01, 2019, 07:41:30 pm »
Hi Honglue,

I've fixed the bug in the updated DSSR distribution on the download page. It was due to the relaxed definition of WC pairs to account for distorted geometry, which causes problems in a special case like yours.

Please have a try and report back how it goes. I'm planning to release DSSR tomorrow if no other issues pop up.

Best regards,

Xiang-Jun

21
RNA structures (DSSR) / Re: strange exception
« on: June 30, 2019, 09:05:03 pm »
Hi Honglue,

I can reproduce the reported issue. It is likely a bug in the code for ordering loop nucleotides in a special case. I will look into the issue and get it fixed (hopefully) shorty. Stay tuned.

Thanks for reporting.

Xiang-Jun

22
General discussions (Q&As) / Re: examples
« on: June 29, 2019, 01:34:22 pm »
Quote
handling file <fiber31.pdb>
open_tmpfile() failed: Permission denied

This error message means you do not have written permission to create a temporary file (by calling C function
"tmpfile()"). This is very unusual, and certainly the first time I've heard of such a case. Without contextual info, I cannot provide much further help.

Xiang-Jun

23
"Cover image featuring the web 3DNA 2.0 paper" title="Cover image featuring the web 3DNA 2.0 paper"

Caption: Examples of customized molecular models that can be generated with 3DNA: (top) a chromatin-like, nucleosome-decorated DNA with the structures of known histone-DNA assemblies placed at user-defined binding sites; (lower left) molecular schematic of a DNA trinucleotide diphosphate illustrating the base planes and reference frames used to construct and analyze 3D nucleic acid-containing structures; (lower right) customized single-stranded tRNA model built from a user-defined base sequence and a set of rigid-body parameters describing the desired placement of successive bases. Color code of base blocks: A, red; C, yellow; G, green; T, blue; U, cyan.



The top image is as Fig. 1E, and the lower-left image is as Fig. 2A. The lower-right image is sort of like Fig. 1D. However, it was actually generated using DSSR and PyMOL with (long) base-pair blocks for Watson-Crick pairs, with he commands used listed below:

Code: Bash
  1. x3dna-dssr -i=1fir-rebuild.pdb --blocview --block-opts=wc-minor -o=1fir-raw.pml
  2.  
  3. # Manually re-oriented the block image: "turn z, -155", and
  4. #     changed the chain color from "red" (default for chain A) to "marine"
  5. #     ray-traced and rendered to a PNG image, "1fir-dssr-pymol.png".
  6. # The revised PYMOL .pml file is named "1fir-dssr.pml"
  7. pymol -qkc 1fir-dssr.pml
  8. # The above PyMOL command generates "1fir-dssr-pymol.png", which is trimmed as below
  9. convert -trim +repage -transparent white 1fir-dssr-pymol.png 1fir-dssr.png

The following key related files are attached:
  • 1fir-rebuild.pdb -- a tRNA model generated with web 3DNA 2.0
  • 1fir-raw.pml -- the PyMOL script crated with DSSR (line #1 above)
  • 1fir-dssr.pml -- manually edited PyMOL script based on 1fir-raw.pml
  • 1fir-dssr.png -- the schematic block images used in the cover image

24
General discussions (Q&As) / Re: 3DNA download issue
« on: June 26, 2019, 12:52:33 pm »
Please cheak FAQ: "How to make the best use of the Forum?"

Did you click the download link in the member-only page?

Xiang-Jun

25
Hi Shuxiang,

Quote
A lot of "&"s  are inserted in sequence and dot-bracket notation. It looks like a bug for the output.

It is not a bug, but a feature in DSSR. Read "3.18.12 The --dbn-break option" in the DSSR manual.

For this special case, the atomic model is in bad geometry (even though it has a nominal resolution of 3.7 Å). See the attached image for nucleotides 1-3 (GGU) of chain 3. This is sort of like the 3DNA-rebuilt models with an approximate backbone conformation that needs to be optimized (using Phenix as shown in our web 3DNA 2.0 paper).

You could use "--dbn-break=no" to remove the & symbols, as documented in the DSSR manual.

Best regards,

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.