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NAME
analyze - calculate nucleic acid structural parameters
SYNOPSIS
analyze [OPTION] FILE ...
DESCRIPTION
calculate various nucleic acid structural parameters (propeller,
slide, roll, twist, backbone torsions etc.) from FILEs, and
generate input to other utility programs. As of v2.1 with the
-torsion option, it also provides detailed pseudo-torsions, Zp
for single-stranded DNA/RNA structures, and classification of
backbone BI/BII and base syn/anti-conformation
-c output structural parameters between helical regions
("----" by default). The same effect can be achieved by
directly modifying the input file (change "9" or "1" to
"0" in the third column of each base pair list.)
-t detailed (pseudo) torsions, BI/BII, syn/anti- and Zp
-h this help message (any non-recognized options will do)
INPUT
given a PDB file "sample.pdb", the input to analyze can be most
conveniently generated with the utility program find_pair:
find_pair sample.pdb sample.inp
an explicit input file (including 'stdin') must be specified.
EXAMPLES
analyze sample.inp
analyze sample1.inp sample2.inp sample3.inp
find_pair sample.pdb stdout | analyze stdin
find_pair sample.pdb stdout | analyze -c stdin
analyze -t=6tna.tor 6tna.pdb
OUTPUT
sample.out, auxiliary.par, bp_step.par, bp_helical.par,
cf_7methods.par, ref_frames.dat, poc_haxis.r3d, stacking.pdb
hstacking.pdb
SEE ALSO
find_pair, rebuild, frame_mol, ex_str, stack2img, cehs
AUTHOR
3DNA v2.1-2014dec22, created and maintained by Xiang-Jun Lu (PhD)
Please post questions/comments on the 3DNA Forum: http://forum.x3dna.org/
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But still my biggest concern remains that the order of base-pairs or maybe name of them is changing in different snapshots. For example base-pair 169 in '29999.par' is C-G but in '30000.par' is G-C. Do you know why that happens? If they were in a goos order, at least I could find out which base-pair is highly deformed that cannot be understood by 3DNA.The different order is because of the fact that the structures are distorted in different ways, and the 'find_pair' algorithm is not smart enough to figure out which way to go, and 'randomly' picks one based on its default settings. If you do your MD analysis as suggested, this won't become an issue: you need to generate an initial input using any frame with find_pair and edit it as necessary. Think of the scenario where you do not have access to find_pair.
Just want to make a suggestion which I think might be helpful for MD analysis in general. It would be better if 3DNA had the option of skipping those pdb input files presented in the pdb_list and just gave a warning that for example this pdb contains distorted base-pairs and then resumed analysis of the rest of the files. Otherwise, one needs to run it and checked any time for all the distorted files in a trajectory.
--errlog, -g: Print error message instead of abort programx3dna_ensemble analyze -b inp.inp -p 'pdbs/frame106*.pdb' -gProcess PDB file pdbs/frame1066.pdb 1 / 3
Process PDB file pdbs/frame1067.pdb 2 / 3
Error in running command: '/Users/xiangjun/X3DNA/bin/analyze -c temp_model.inp 2> msgfile'
Process PDB file pdbs/frame1068.pdb 3 / 3Funded 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