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Let me ask around the lab and get their input and I'll make a suggestion based on what they suggest that would be most "user-friendly" and easily readable.That's great -- once I get your feedbacks, I will implement them in the next beta release of DSSR. I'm planning to add some new features to DSSR, including detection of kink-turns, but would take priority on refinements of existing functionality.
55 asymmetric internal loop: 7 nts; [1x2]; linked by [#168, #169]I like your idea for internal loop. Maybe stem loop, bulge, and junctions can follow the same pattern?
1 loop bases [A]; 0.G2855+(0.A2856)+0.C2857 [G(A)C]
2 loop bases [CA]; 0.G2900+(0.C2901+0.A2902)+0.C2903 [G(CA)C]
List of 12 bulge(s)
1 bulge: 6 nts; [2x0]; linked by [#19, #-8]
0.C245+0.G246+0.A247+0.A248+0.U265+0.G266 [CGAAUG]sel.pdb
sel-all.out
2 # duplex
12 # number of base-pairs
1 1 # explicit bp numbering/hetero atoms
1 24
2 23 0 # 1 | ....>A:...2_:[..G]G-----C[..C]:..23_:B<.... 0.51 0.33 9.29 9.08 -3.37
3 22 0 # 2 | ....>A:...3_:[..C]C-----G[..G]:..22_:B<.... 1.01 0.90 38.28 8.76 -0.28
4 21 0 # 3 | ....>A:...4_:[..G]G-----C[..C]:..21_:B<.... 0.62 0.42 8.68 9.05 -3.12
5 20 0 # 4 | ....>A:...5_:[..A]A-----T[..T]:..20_:B<.... 0.34 0.07 24.63 9.03 -1.29
6 19 0 # 5 | ....>A:...6_:[..A]A-----T[..T]:..19_:B<.... 0.44 0.14 27.81 9.19 -2.88
7 18 0 # 6 | ....>A:...7_:[..M]c-----G[..G]:..18_:B<.... 0.60 0.39 16.09 8.90 -2.81
8 17 0 # 7 | ....>A:...8_:[..G]G-----C[..C]:..17_:B<.... 0.19 0.02 12.30 9.07 -4.15
9 16 0 # 8 | ....>A:...9_:[..C]C-----G[..G]:..16_:B<.... 0.50 0.35 15.49 9.12 -3.03
10 15 0 # 9 | ....>A:..10_:[..G]G-----C[..C]:..15_:B<.... 0.13 0.09 12.22 9.02 -4.07
11 14 0 # 10 | ....>A:..11_:[..C]C-----G[..G]:..14_:B<.... 0.49 0.40 12.81 9.03 -3.07
12 13 0 # 11 | ....>A:..12_:[..G]G-----C[..C]:..13_:B<.... 0.44 0.06 25.76 8.98 -3.15
find_pair sel.pdb bpfile.dat
analyze bpfile.dat
x3dna_ensemble analyze -b bpfile.dat -p sel.pdb -o ensemble.out
x3dna_ensemble extract -p shift
****************************************************************************
Local base-pair step parameters
step Shift Slide Rise Tilt Roll Twist
1 GC/GC 1.29 0.44 2.62 6.32 -3.86 31.01
2 CG/CG -1.11 -0.04 3.86 -6.40 14.10 35.74
3 GA/TC 0.78 -0.30 3.57 -0.97 2.92 36.20
4 AA/TT -0.44 -0.77 3.48 -0.74 2.14 35.20
5 Ac/GT 0.00 0.04 3.09 2.14 0.76 39.12
6 cG/CG 0.68 0.41 3.21 -2.61 17.38 29.80
7 GC/GC 0.40 -0.35 3.28 -0.47 0.89 32.94
8 CG/CG -0.64 0.39 3.04 3.76 9.39 29.46
9 GC/GC -0.36 -0.89 3.40 -6.53 1.69 37.52
10 CG/CG 0.93 -0.64 3.45 2.40 10.67 32.12
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. 0.15 -0.17 3.30 -0.31 5.61 33.91
s.d. 0.78 0.50 0.34 4.16 6.84 3.33
sel 1.29 -1.11 0.78 -0.44 0.00 0.68 0.40 -0.64 -0.36 0.93 Here the first column ('sel') is the name of the PDB file (without extension), and the next 10 columns are the shift values for the 10 dinucleotide steps. Since your pattern is very specific, it matches only one PDB file ('sel.pdb').fiber -seq=aaatttt -single fb.pdb1. When I run the command "find_pair sample_md0.pdb bpfile.dat", the output file bpfile.dat is different from the one given initially. For example, this file has 13 base pairs as opposed to 12 base pairs in the initial file.I noticed you said this is ok in your post which I referred in the first message.That's understandable. The point of creating a bpfile explicitly is to provide flexibility as to which bps to analyze. If you run find_pair on each frame of a MD trajectory, the identified bp info may be different.
2. I am assuming the sample_md0.pdb is generated from the initial frame of the trajectory. For example, I have a trajectory consisting of 5000 frames and I am analysing all frames except the first 999 frames. So in this case, the file equivalent to sample_md0.pdb, will be the pdb file corresponding to 1000 frame.The file 'sample_md0.pdb' is provided by a 3DNA user, and I've used it as a test case in developing the x3dna_ensemble script. The ensemble file contains 21 models (numbered 0,1,..20) delineated with MODEL/ENDMDL in PDB format. The content of the file is entirely up to you. The x3dna_ensemble script will analyze each model sequentially.
3. Now for the next step,You can put anything there. The post "Using Glob with Directories" may be helpful to you.
x3dna_ensemble analyze -b bpfile.dat -p 'pdbdir/model_*.pdb' -o ensemble.out
All the model_*.pdb files in the pdbdir are pdb files created for different frames (or timesteps)?
I am assuming this step works for just one frame also. Since my system contains water, and other ions, and I am writing a pdb file for each frame just selecting the dan alone.
Separating by chars vs. integers would be okay, but some alt. residues have numbers in them which makes it more difficult.Could you provide some specific cases to make your point clearer?
Is there any way you would want to add another separator for base type from base number?I'd like to keep the default settings for DSSR simple/succinct, targeting more towards human apprehension than computer parsing. That said, I may consider to add an option to make the id string software friendly.
Ex. "0.C_309" or the like?
/usr/bin/env: ruby: No such file or directoryIt seems you do not have Ruby installed on your machine. What happens if you issue the following command:
rubyHETATM 9998 XS X X 999 68.227 2.641 -26.513Those pseudo HETATM records are just the two end points one helix passes through. As shown in the bending angle FAQ, The normalize helical axis is:
HETATM 9999 XE X X 999 67.797 -2.012 34.748
Helix: -0.007 -0.076 0.997
With the two HETATM records, one can easily add them into the original PDB file to display the helical axis using a molecular graphics programs (e.g., RasMol, Jmol or PyMOL). Moreover, the two helix vectors can be used to reorient the original PDB structure into a view so that one helical fragment lies along the x-axis, and the other in the xy-plane. As documented in detail in recipes #4 on "Automatic identification of double-helical regions in a DNA–RNA junction" of the 2008 3DNA Nature Protocols paper, "The chosen view allows for easy visualization and protractor measurement of the overall bending angle between the two relatively straight helices."
we use the equation given below to solve the problem and we were unsuccessful. ...Could you be specific on how you "were unsuccessful"? What vectors did you use and what result bending angle did you expect?
I am sure that some other things will have to be detected in RNA structuresYes, other things can be detected in RNA structures, and DSSR has laid the basis (a framework) for more features to be built upon.
and for that we really need the maximum of info and your software is a great tool for this.
Thus, providing another output type seems a great option and I suggestOkay, I will add a new option in DSSR beta r11 that puts all pair-wise nucleotide interactions (pairing or non-pairing, with various types of H-bond) in one file. Any suggestion for a name of the option? How about --pair-wise-nt-interactions? Note I am busying right now to meet a deadline, but should be able to get the proposed work done by next week.
a roughly identical file format where in the first section only base base interactions are listed
and where base-backbone and backbone-backbone interactions appear in the "non-pairing interaction" list
which could be labeled more appropriately "Base-base and base-backbone interactions".
# download 1msy.pdb from RCSB PDB; note the -r option to specify the output file "1msy.r3d"
blocview -r 1msy.r3d 1msy.pdb
# run pymol from command line with script "1msy.pml" (see below)
pymol -qc 1msy.pml
load 1msy.r3d
bg_color white
set depth_cue=0
set ray_trace_fog=0
ray 1200,1200
png 1msy.png, dpi=300
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University