Messages

151

General discussions (Q&As) / Re: Setting up 3D-DART with X3DNA

« on: May 28, 2020, 12:46:39 am »

The attached file "x.out" has the following content:

handling file <struct_1_fixed.pdb>

Time used: 00:00:00:00
This structure has broken O3' to P[i+1] linkages
missing ' P  ' atom : residue name 'THY', chain B, number [  27 ]
missing ' OP1' atom : residue name 'THY', chain B, number [  27 ]
missing ' OP2' atom : residue name 'THY', chain B, number [  27 ]
missing ' P  ' atom : residue name 'THY', chain B, number [   1 ]
missing ' P  ' atom : residue name 'THY', chain B, number [  27 ]

This means 3DNA v2.4.4 itself is running properly.

However, the file also contains "EnergyPDNA.exe: command not found". EnergyPDNA.exe is not part of 3DNA, v1.5 or v2.x. It could be part of 3D-DART.

From 3DNA v1.5 to v2.x, there is indeed reorganization of data folders, including:

Code: [Select]

BASEPARS ---> config
Examples ---> examples
FIBER ---> fiber
The most important one is BASEPARS ---> config.

For your convenience, I have dug out 3DNA v1.5, and sent you an email with links for download.

Note that 3DNA v1.5 is no longer supported. Even 3DNA v2.x is under maintenance mode: no more new features, only bug fixes. All new developments are devoted to DSSR and SNAP, which supersede 3DNA.

Best regards,

Xiang-Jun

152

DNA/RNA-protein interactions (SNAP) / Re: Visualization of SNAP output

« on: May 15, 2020, 12:20:17 pm »

SNAP is an analysis tool. Schematic visualization is beyond its design scope.

Have a look of http://skmatic.x3dna.org. Is there anything useful there?

Xiang-Jun

153

RNA structures (DSSR) / Re: Identification of Basepairs - Vertical Seperation

« on: May 15, 2020, 10:10:12 am »

Hi Tom,

Thanks for your interest in implementing the DSSR algorithm for identifying base pairs. You are correct that the two bases in a pair are usually not parallel. Thus the mean the two z-axes is used for calculating the vertical separation (i.e., Rise).

Detailed description of the algorithm can be found in the paper "Structure and Conformation of Helical Nucleic Acids: Analysis Program (SCHNAaP)" (https://doi.org/10.1006/jmbi.1997.1346). The exact algorithm in SCHNAaP was then adapted to 3DNA, and DSSR. The source code of SCHNAaP is available.

Best regards,

Xiang-Jun

154

Feature requests / Re: Mutate_Bases: Option to mutate all residues of the same type to another

« on: May 11, 2020, 12:13:31 am »

As a follow-up of this thread, DSSR 2.0 (to be released soon) contains a new module for in silico base mutations with great flexibility and convenance. It can mutate all of the A's to G's except for residue 5 and residue 7, for example.

The 'mutate_bases' program is obsoleted. No program named 'x3dna-mutate' will be distributed.

Xiang-Jun

155

General discussions (Q&As) / Re: basepair centers

« on: April 28, 2020, 11:43:21 pm »

Hi Daniel,

Thanks for posting an example to make your point clear.

The numerical values you provided for the origins of the two base-pairs at the termini are correct.

I've heard of the term "end-to-end distance of the entire DNA" many times, but never used it in my own work. I'm just wondering what is the end-to-end distance of a circular DNA. Do you have any idea on that?
Best regards,

Xiang-Jun

156

General discussions (Q&As) / Re: basepair centers

« on: April 28, 2020, 06:27:50 pm »

Hi Daniel,

I still need to calculate the end-to-end distance of the entire DNA (or the centers for the corresponding basepairs). Can anyone please help me to obtain this information with x3dna?

Could you please be specific what you mean here, using a concrete example?

Xiang-Jun

157

RNA structures (DSSR) / Re: Identify sugar type in the DSSR output

« on: April 23, 2020, 02:39:19 pm »

I've just updated DSSR to v1.9.10-2020apr23. It has a new field named "nt_type", with possible values of "DNA", "RNA" or "unknown". Since the item is included in the nts[] array, I've used the name "nt_type" instead of your suggested "nt_sugar_type" (with values of "ribose" or "deoxyribose" etc).

Please download the updated DSSR (forget about the label, which still reads "v1.9.9-2020feb06"), and report back how it goes.

Best regards,

Xiang-Jun

158

General discussions (Q&As) / MOVED: Standard Values for A-, B-, C-DNA on w3DNA

« on: April 23, 2020, 09:34:21 am »

This topic has been moved to w3DNA -- web interface to 3DNA.

http://forum.x3dna.org/index.php?topic=909.0

159

w3DNA -- web interface to 3DNA / Re: Standard Values for A-, B-, C-DNA on w3DNA

« on: April 23, 2020, 09:34:04 am »

The question is vague. Please be specific by providing a (minimal) reproducible example.

Thanks,

Xiang-Jun

This question is related to w3DNA not 3DNA per se. I am transferring it to the board "w3DNA -- web interface to 3DNA" from the "General discussions (Q&As)".

160

RNA structures (DSSR) / Re: DSSR issue --json and --analyze

« on: April 20, 2020, 11:39:26 am »

Hi Joe,

Glad to see that helped.

I didn't see that in the documentation.

As I mentioned in several places already, DSSR has (far) more features than documented. The User Manual is already 108-page long, and I doubt few users read it through, not to mention fully understand/appreciate the details. That's understandable. It is better to claim less but deliver more, rather than the other way around. That's just my way of thinking and performing research, at least.

Best regards,

Xiang-Jun

161

RNA structures (DSSR) / Re: DSSR issue --json and --analyze

« on: April 20, 2020, 11:29:04 am »

Hi Joe,

Did you know that the base-pair reference frame info is already available in the JSON output? For example,

Code: Bash

1. # Note the --more option
2. x3dna-dssr -i=355d.pdb --json --more | jq '.pairs[0].frame'
3. # You'll get the following output:
4. {
5.   "rmsd": null,
6.   "origin": [
7.     17.127,
8.     25.962,
9.     25.878
10.   ],
11.   "x_axis": [
12.     -0.987,
13.     0.154,
14.     0.038
15.   ],
16.   "y_axis": [
17.     0.121,
18.     0.886,
19.     -0.447
20.   ],
21.   "z_axis": [
22.     -0.103,
23.     -0.436,
24.     -0.894
25.   ],
26.   "quaternion": [
27.     -0.036,
28.     0.071,
29.     0.971,
30.     -0.228
31.   ]
32. }

Is that what you want?

Xiang-Jun

162

RNA structures (DSSR) / Re: DSSR issue --json and --analyze

« on: April 19, 2020, 11:49:49 pm »

Hi Joe,

Thanks for your kinds words about DSSR ... not all people are appreciative of what I would call a "solid software product". To some "experts", DSSR is a project all done, nothing more worthing to be added.

I added the --analyze mainly to obsolete the analyze program of 3DNA, which is still maintained but no more new features. As documented in the DSSR manual, an alternative form of this option is --3dna-v2. So when the --analyze is enabled, DSSR generates a text output similar to the original 3DNA analyze program. In other words, the DSSR --analyze is working as initially designed.

As always, I'm open to suggestions from users like you. You're the first person (as far as I can recall) who has actually asked a question on this --analyze option in DSSR. What parameters from the --analyze option are missing in DSSR with --json for your project?

Best regards,

Xiang-Jun

163

FAQs / Re: How do I build nucleic acid structures with sugar-phosphate backbone?

« on: April 18, 2020, 08:56:09 pm »

Please provide details. Reproducibility is the key.

Xiang-Jun

164

General discussions (Q&As) / Re: Generating PDB file

« on: April 18, 2020, 08:53:55 pm »

I used the BuildNucleicAcids.py function and mentioned the DNA type and other details. It generated a pdb file without the DNA backbone atoms (attached image).

"BuildNucleicAcids.py" is not part of 3DNA. Please ask the author of the program for support.

Xiang-Jun

165

RNA structures (DSSR) / Re: Documentation of the Json output fields ?

« on: March 13, 2020, 09:24:28 am »

Hi Louis,

I am glad that your read my blogposts and the DSSR User Manual. I am impressed that you do not want recreate the wheel but rely on DSSR for your research projects.

Can you explicitely list which descriptors are certified working as expected and documented, and which i should not use/publish in my future work ? I just want to avoid the situation where my work strongly depends on something experimental and not citable. I am not gonna implement your ideas

As you quoted from my previous response,

Overall, I do want to ensure what have been documented and published to be accurate and reproducible.

Please take what have been published and documented in the DSSR User Manual as certified by me. Note that some of the documented features, e.g., the section on "Splayed-apart conformations" (which are novel and unique to DSSR), have not been published.

Please do cite the 2015 NAR DSSR paper, even for those documented but unpublished features. I may publish more papers on specific features from DSSR, just I did with the DSSR-Jmol integration. No matter what else, the NAR'15 paper is the fundamental one to cite for any DSSR-related applications.

Best regards,

Xiang-Jun

166

General discussions (Q&As) / Re: Support for batch processing?

« on: March 10, 2020, 02:02:31 pm »

Hi,

You could use file redirections for batch process. Or try other available tools that may be able to do this job better. If I could receive continued funding support, I will improve the 3DNA "fiber" command for applications like this. Nowadays, such feather enhancements are treated as "incremental" (not "novel"), and I may no longer be able to continuously support the community.

Best regards,

Xiang-Jun

167

General discussions (Q&As) / Re: Convert RNA hairpin into DNA

« on: March 04, 2020, 10:11:58 am »

converting the ribose into deoxyribose (removing the O2')

That should be an easy task, right? Together with the U-->T base mutations, the answer to "Convert RNA hairpin into DNA" should be "clean", even if performed manually.

Could you provide a concrete example to show unambiguously the requirements?

It is essential that you provide your "manual" result, in whatever no so clean way.

Often times, I wonder how difficult it is to provide a minimal reproducible example that can unambiguously illustrate the question asked.

Xiang-Jun

168

RNA structures (DSSR) / Re: Documentation of the Json output fields ?

« on: March 03, 2020, 12:06:04 pm »

Hi Louis,

Thanks for your questions on descriptions of the DSSR JSON output. As you noticed, DSSR derives (far) more features than those already documented in the 108-page User Manual. That's on purpose. DSSR contains many unpublished results, as well as a lot of experimental functionalities. On the other hand, some features already documented in the DSSR User Manual may not have been read as I'd expect. Overall, I do want to ensure what have been documented and published to be accurate and reproducible.

For nucleic acid structures, see "Principles of Nucleic Acid Structure" by Wolfram Saenger. For 3DNA/DSSR, read the 2003 NAR paper on 3DNA, and 2015 NAR paper on DSSR and the DSSR User Manual.

Best regards,

Xiang-Jun
 

169

General discussions (Q&As) / Re: Convert RNA hairpin into DNA

« on: March 03, 2020, 11:32:29 am »

The idea is for example to convert the RNA hairpin in 1F27 (extracted and atttached with this post), into DNA, thus converting Uinto T (feasible with mutate), but also altering the backbone's ribose.

As you noted above, the U-->T conversion can be achieved via mutate_bases. This part is clear (to me). However, I still cannot fully understand what you mean by "also altering the backbone's ribose". Idealized DNA sugars can have C2'-endo (B-DNA) or C3'-endo (A-DNA) conformations. In real PDB structures, there are many intermediate sugar puckering as well.

This can be done "manually", but in a not so clean way, imo.

There is no magic in writing a program to "automate" this process: it is all based on a thorough understanding of the mechanics. It is essential that you provide your "manual" result, in whatever no so clean way. I may then be able to help you (and others in a similar situation) by implementing such a feature in 3DNA.

Best regards,

Xiang-Jun

170

General discussions (Q&As) / Re: Convert RNA hairpin into DNA

« on: March 02, 2020, 11:27:56 am »

Hi DML,

Thanks for posting your question on the 3DNA Forum. I understand what you're asking for conceptually. Could you provide a concrete example to show unambiguously the requirements? In writing a useable code, every detail needs to be taken into consideration. 3DNA/DSSR may already have some basic components that could be tailored to your purpose.

Best regards,

Xiang-Jun

171

RNA structures (DSSR) / Re: Running 1ehz example: issue .ntParams

« on: February 28, 2020, 06:47:17 pm »

Hi Jason,

Good catch! The key ntParams in the DSSR JSON output was changed to nts a long time ago. However, the manual has not been updated accordingly. That's why you got the "null" output since the JSON file does not contain any objects named ntParams.

Simply replace .ntParams by .nts in the commands listing would resolve the issue. The DSSR Manual has now been corrected.

Best regards,

Xiang-Jun

172

RNA structures (DSSR) / Re: Calculate base step parameters manually

« on: February 22, 2020, 06:52:57 pm »

Hi,

The "unexpected dichotomy" of twist in your MD data is sort of understandable based on my experience: they could be due to a flip of base-pair reference frame. However, given the limited information provided, it is impossible to decipher where the issue is. As always, it helps to provide a minimum example that can reproduce the reported issue.

For details on how 3DNA parameters are calculated, please see $X3DNA/doc/tech-details.pdf and the 3DNA 2.4 source code. Check also the supplementary PDF of the paper "Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures": http://docs.x3dna.org/w3DNA2.0/w3DNA2.0-supp.pdf.

Best regards,

Xiang-Jun

173

RNA structures (DSSR) / Re: Problem using --pair-list options

« on: February 14, 2020, 10:30:52 am »

Hi Ángel,

It finally worked thanks to the change of the input name.

Glad to hear that DSSR works as expected with a change of the input file name to the --pairs-list-inpfile option.

Each time DSSR runs, it remove a long list of files (e.g., dssr-pairs.pdb, dssr-multiplets.pdb etc.) that can be automatically created by default. This design ensures a clean state for each DSSR run. As a result, users should name an input file differently than the default to avoid it being removed or overwritten.

Thanks Xiangjun for the fast and precise response, im going to share you via e-mail the pdb file of our structure so you can check the base pair recognision, but it works fine with the --pair-list option.

I've quickly checked the PDB file you emailed me. DSSR is working as expected for your structure: using the U11-U38 'pair' as an example, they are too far apart to be termed a pair in the conventional sense. The shortest O...O or O...N distances is around 6 angstrom, much longer than even the generous 4.0 A cutoff for H-bond used in DSSR. That's why DSSR does not detect them. The DSSR --pair-list options have been designed precisely for a usecase like yours.

Best regards,

Xiang-Jun

174

RNA structures (DSSR) / Re: Problem using --pair-list options

« on: February 12, 2020, 01:51:56 pm »

As a follow-up, I've updated the DSSR User Manual with a caveat on the default file name dssr-pairs.txt with --pairs-list option variants. Hopefully, the instruction is now clear enough so that users would not employ the default OUTPUT file name for INPUT to DSSR.

Even before the update, the DSSR manual deliberately used the name my-pairs.txt with --pair-list-outfile and --pair-list-inpfile (as shown in my previous response). However, the message was presumably too subtle to be noticed by first-time users.

Best regards,

Xiang-Jun

175

RNA structures (DSSR) / Re: Problem using --pair-list options

« on: February 12, 2020, 12:18:22 pm »

Hi angel,

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

First of all thank you for developing this software, but we are having some troubles using the --pair-list options. We have tried the examples presented on the manual but doesn't work neither (using last version of X3DNA).

As documented in the DSSR manual, there are three variations to the DSSR --pair-list option:

• By simply specifying the --pair-list option, DSSR will output an additional auxiliary file, named dssr-pairs.txt by default.
  x3dna-dssr -i=1msy.pdb -o=1msy.out --pair-list # --> 'dssr-pairs.txt'
• The name of output pairs list can be customized via the --pair-list-outfile=NAME option, as shown below.
  x3dna-dssr -i=1msy.pdb -o=1msy.out --pair-list-outfile=my-pairs.txt
• User-supplied list of pairs can be specified via the --pair-list-inpfile=NAME option. In such cases, DSSR will use these customized bps instead of identifying them ab initio.
  x3dna-dssr -i=1msy.pdb --pair-list-inpfile=my-pairs.txt

There should be no space between --pair-list and -inpfile in the --pair-list-inpfile=NAME option. Otherwise, DSSR would take --pair-list as an option (the first case) and -inpfile as another option. The default dssr-pairs.txt file should not be used as the input file name via --pair-list-inpfile=NAME.

The generation works well, the problem is at the moment to introduce through:
       x3dna -dssr -i=1msy.pdb  --pair-list -inpfile=dssr-pairs.txt
It says:
       open_file <dssr-pairs.txt> failed: No such file or directory

I'm assuming that in the example, x3dna -dssr means x3dna-dssr, and --pair-list -inpfile=dssr-pairs.txt means --pair-list-inpfile=dssr-pairs.txt (i.e., no spaces). The following commands work as expected:

Code: Text

1. x3dna-dssr -i=1msy.pdb  --pair-list-outfile=my-pairs.txt
2. # edit 'my-pairs.txt' as needed
3. x3dna-dssr -i=1msy.pdb  --pair-list-inpfile=my-pairs.txt

The problem is with the default file dssr-pairs.txt used as input. I'll update the user manual shortly. Any suggestions on how to make the point clear, based on your experience?

We have a non-canonical RNA structure with some mismatches U-U that aren't recognised automatically

Could you share with us an example U-U pair that is not automatically recognized by DSSR? A fragment with atomic coordinates of such an U-U pair would be fine. You may also send me such a data file by email. I'm interested in improving the default DSSR options in as many cases as pragmatically applicable.

Best regards,

Xiang-Jun