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.
This section allows you to view all posts made by this member. Note that you can only see posts made in areas you currently have access to.
Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Licensing · Video Overview· RNA Covers
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.
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
Overall, I do want to ensure what have been documented and published to be accurate and reproducible.
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)
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.
analyze -t=/path/to/pseudotorsions/folder/4v8p[1]-B3.tor /path/to/chains/folder/4v8p[1]-B3.pdb
Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.