Messages

1

RNA structures (DSSR) / Re: Bug or feature (?) : residue numbering not understood

« on: June 01, 2021, 04:41:20 pm »

Yes, this is what i expect.

2

RNA structures (DSSR) / Re: Bug or feature (?) : residue numbering not understood

« on: June 01, 2021, 02:56:31 pm »

Hi,

The page works in Chromium and Chrome, works in Opera, and does not work in Firefox, Edge, or Vivaldi. I have no macOS computer to test Safari, sorry.

Louis

3

RNA structures (DSSR) / Re: Bug or feature (?) : residue numbering not understood

« on: May 31, 2021, 11:22:09 am »

Dear Xiang-Jun, dear CTV team,

Attached to this post a screenshot of the page at URL http://innovation.columbia.edu/technologies/CU20391/ when i open it in Mozilla Firefox (tested on Linux and Windows 10) or Microsoft Edge (Windows 10).
Firefox version : 88.0.1 (but i had the same issue in past months with past versions)
Edge version : 91.0.864.37 (but same)


(Also notice the lack of HTTPS.)

Hope this helps,

Louis

4

RNA structures (DSSR) / Re: Bug or feature (?) : residue numbering not understood

« on: May 27, 2021, 12:07:31 pm »

Hi Xiang-Jun,

Thanks for the copy-paste. I will discuss with my team, but yes, we may go for it.
If the CTV team wants more information on the problem, do not hesitate to ask me (i tried with different browsers, but nothing succeeds).

Louis

5

RNA structures (DSSR) / Re: Bug or feature (?) : residue numbering not understood

« on: May 27, 2021, 04:45:11 am »

Hi,

Thank you for the quick fix !

I have an academic licence for DSSR2, but i can consider "DSSR Pro", what is the difference and how much does it cost ? (The CTV website displays a blank page)

Due to a lack of funding support, this is the only way my effort on DSSR can be justified. I will ensure that paid users always receive top-notch support.

I understand. While i entirely trust you since you have demonstrated efficiency and skills in developping DSSR and quickly replying to questions on this forum, the CTV is not very engaging, since the website regularly has issues. My first visit was in September 2020, blank page, I had to ask techventures<at>columbia.edu by email to fix it. And today i have the same issue. And i could read in the forum that other people faced problems.
I suggest you summarize the content of the page in a forum post, to provide a reliable source of information about DSSR licensing, maybe ?

6

RNA structures (DSSR) / Bug or feature (?) : residue numbering not understood

« on: May 26, 2021, 12:33:10 pm »

Dear Dr Xiang-Jun,

About residue numberings. After annotating a structure, outputing in JSON, looking at the "nts" section, residues are organized by chain, and within a chain, the "index_chain" field starts at one (expected behavior, very good). However, in some cases, it starts at last chain's last index_chain plus one, is there any reason for that ?

My spotted case is 4w29 (a large ribosome), i am looking at chain BA, which starts with index_chain = 77, following chain AX's index_chain = 76.
I checked, the chains are not contiguous in space, nothing indicates they could be linked together. Other chains in the structure start at 1.

Execution output below (nothing special spotted), using DSSR v1.9.9:
$ x3dna-dssr -i=/home/persalteas/Data/RNA/3D/RNAcifs/4w29.cif --json --auxfile=no > 4w29.json

Code: [Select]

Processing file '/home/persalteas/Data/RNA/3D/RNAcifs/4w29.cif'
[i] '/home/persalteas/Data/RNA/3D/RNAcifs/4w29.cif' taken as in .cif format by file extension.
  1.AA.U.434 0.121
  1.AA.U.723 0.121
  1.AA.U.1126 0.135
  1.AA.U.1301 0.123
  1.AW.U.8 0.123
  1.BA.U.1939 0.122
  1.BA.U.2887 0.121
  1.CA.U.68Q 0.126
  1.CA.U.669 0.123
    total number of nucleotides: 9398
    total number of amino acids: 14040
[w] arginine [AD.ARG3] -- NH1/NH2 naming swapped
[w] arginine [AD.ARG118] -- NH1/NH2 naming swapped
[w] arginine [AT.ARG89] -- NH1/NH2 naming swapped
[w] arginine [AY.ARG351] -- NH1/NH2 naming swapped
[w] arginine [AY.ARG354] -- NH1/NH2 naming swapped
[w] arginine [AY.ARG357] -- NH1/NH2 naming swapped
[w] arginine [AY.ARG396] -- NH1/NH2 naming swapped
[w] arginine [AY.ARG484] -- NH1/NH2 naming swapped
[w] arginine [AY.ARG504] -- NH1/NH2 naming swapped
[w] Residue AV.G1 missing planar atom [ C8 ]
    total number of base pairs: 4601
    total number of multiplets: 620
    total number of helices: 263
    total number of stems: 601
    total number of isolated WC/wobble pairs: 151
    total number of atom-base capping interactions: 589
    total number of splayed-apart dinucleotides: 1238
                        consolidated into units: 797
    total number of hairpin loops: 228
    total number of bulges: 118
    total number of internal loops: 245
    total number of junctions: 116
    total number of non-loop single-stranded segments: 73
    total number of kissing loops: 13
    total number of A-minor (types I and II) motifs: 191
    total number of eXtended A-minor (type X) motifs: 219
    total number of ribose zippers: 94
    total number of kink turns: 29
[w]  number-of-residues=658 -- in shortened form
[w]  number-of-residues=658 -- in shortened form
[w]  cross-paired segments in separate chains, be *careful* with .dbn

Time used: 00:00:02:56
Thanks,

Louis

7

RNA structures (DSSR) / Do you provide DSSR 1.* downloads ?

« on: September 15, 2020, 08:38:20 am »

Hi xiangjun,

Do you provide downloads of old versions ? I published using v1.9.9 and need to ensure reproductibility.
If not, do you allow us to embed the executable in a larger software container (e.g. Docker) ? The DSSR functionalities will not be available from outside the container.

I also could ensure my work gives the same results with DSSR 2.0, which is probably the case, but the CTV licensing page is empty (issue ? maintenance ?).
EDIT: (for people reading this in the future): Disable your ad blocker so that the page's content loads correctly.

What is the best thing to do ?
Thanks,

Louis

8

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

« on: March 13, 2020, 04:14:26 am »

Hi xiangjun,

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

Okay, i can understand. However, i found answers in your blog posts, may it help some future reader:

• Conformation of the sugar ring in nucleic acid structures
• Two slightly different definitions of sugar pucker
• Torsion angles of nucleic acid structures
• Ctrl+F "splay" and "reference frame" in the manual

Now that i understand a bit more, i think some will be relevant to me. I am building a dataset with as many descriptors per nucleotide as possible to do some feature selection and machine-learning predictions.
So i wish i could include all the sugar conformation descriptors, glyco-bond and backbone conformations, and in general, all what applies to a single nucleotide.

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

Thanks a lot,

Louis

9

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

« on: March 03, 2020, 05:25:07 am »

Hello,

I noticed DSSR's json output of a structure analysis gives a lot of information (about individual nucleotides in particular), and i do not know (yet) all their meanings.
I searched a bit for a documentation, but the manual does not provide the fields descriptions.

The list of fields i am talking about:

index
index_chain
chain_name
nt_resum
nt_name
nt_code
nt_id
dbn
summary (and there are several fields inside)
alpha, beta, gamma, delta, epsilon, zeta
epsilon-zeta
bb_type
chi
glyco_bond
C5prime_xyz
P_xyz
form
ssZp, Dp
splay_angle, splay_distance, splay_ratio
eta, theta, eta', theta', eta_base, theta_base
v0, v1, v2, v3, v4
amplitude
phase_angle
puckering
sugar_class
bin
cluster
suiteness
filter_rmsd
frame (several descriptors)

In particular, i am interested in the following points:

• Why are we interested in the C5' XYZ position ?
• What are the "splay" descriptors ?
• What are the v0-v4 descriptors ?
• What is the difference between sugar_class and puckering ?
• What is the frame, and the RMSD value provided ?

I am mostly trying to learn more, if such documentation does not exist (yet), i welcome some bibliography references if you have some...

Thanks a lot for your time,

Louis

10

RNA structures (DSSR) / Re: Batch-processing structures with analyze -t

« on: January 06, 2020, 05:06:43 pm »

Thanks, this is actually much simple, faster and convenient.

I never noticed the eta_prime and theta_prime fields in the json output until now.
Thanks Markus for the R script too, but i won't need it, it is actually three lines of python:

Code: [Select]

import json, subprocess

filename = "/path/to/your/RNA/chain.pdb"

output = subprocess.run(["x3dna-dssr", f"-i={filename}", "--json", "--auxfile=no"], stdout=subprocess.PIPE, stderr=subprocess.DEVNULL)
nts = json.loads(output.stdout.decode('utf-8'))["nts"]
for nt in nts:
    print(nt["nt_resnum"], '\t', nt["eta_prime"], '\t', nt["theta_prime"])  # or whatever you want to do with them.

My issue is solved, thanks a lot, Xiang-Jun !

11

RNA structures (DSSR) / [Solved] Batch-processing structures with analyze -t

« on: January 06, 2020, 09:42:06 am »

Hi there,

First, thank you a lot to each and everyone of you developing DSSR, this is an awesome piece of software that perfectly suits my needs. I already use it for some time without any problems. Today, i have a technical question to enhance my productivity.

I am trying to "analyze -t" a few thousands of RNA chains to get their eta' and theta' pseudotorsions, which works very well. So, i use several threads which run analyze in parallel, on a multicore CPU.

The fact is "analyze -t" creates a file named Borg_P_C1_C4.dat with the cartesian coordinates of the atoms used. As we cannot control this file's name, i am afraid of conflicts between my threads, each of them trying to read/write different content into the same file.

Therefore, two questions:

• Is the .dat file necessary to compute the .tor file, or the opposite ?
• Is there a way to control that file's name ?

Example command i run:

Code: [Select]

analyze -t=/path/to/pseudotorsions/folder/4v8p[1]-B3.tor /path/to/chains/folder/4v8p[1]-B3.pdb
Thanks a lot for your help,

Louis Becquey
PhD Student @Univ Evry, Université Paris-Saclay