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So I was wondering if 3DNA can give information on which base exactly is fluctuating more causing the opening in the pair ?No. 3DNA "can give information only on a base pair in this case".
if I can calculate the DNA bending during the simulation timeNo.
or I will need to find an average structure of my simulation and calculate the bending of that structure.It is entirely up to you. Please remember that 3DNA is just a tool set.
.Importantly, for the [mono:2fyxsqwq]-e[/mono:2fyxsqwq] and [mono:2fyxsqwq]-m[/mono:2fyxsqwq] options, each model in the ensemble must be delimited by an MODEL/ENDMDL pair, as clearly documented in the Coordinate Section of the PDB format.The commonly used ensemble formats are better and easily handled on a case-by-case basis, with the following three choices:
After I submitted my reply, I already changed the line to have the snapshots as numbers only in your script. Still, I think it is better to have the numbers as default. May be in your next version?Suggestion taken -- now in v0.3, the first column is just the snapshot number, without the [mono:2688raft]model_[/mono:2688raft] prefix.
By distribution calculation I meant in addition to the means, standard deviations you already supply, it would be nice to have BI/BII distributions averaged over the trajectory, histograms of each parameter (per base pair/base pair step and over the whole structure). I know there is no perfect analysis script/program out there, but the more the initial analysis does the better for the end user. It also encourages people to use it more!Just to clarify, the scripts currently do not provide mean/std etc statistics -- they are intended to be calculated by the users, using R/Matlab/Octave/Excel etc. Regarding BI/BII classification of backbone, histograms of parameters etc, I am putting them in my to-do list.
One more suggestion: In the simulations there are always end effects. A general practice among MD people is to remove the first and last base pairs from the analysis to reduce these effects in the subsequent analysis. It would be great to have this option available as a choice in the script.Suggestion taken -- now v0.3 has a new [mono:2688raft][red:2688raft]-e[/red:2688raft][/mono:2688raft] option to accomplish just what you asked. Moreover, the two ends can be asymmetrical, e.g., [mono:2688raft][red:2688raft]-e 1 2[/red:2688raft][/mono:2688raft] to remove the first and the last two bps from the extracted parameter list.
I am using the program to analyze drug-DNA MD simulations and would like to plot base pairs vs Twist (or Rise or Roll) values and therefore I would like to find an average of those values for each base pair over the simulation. Does bp_helical or bp_step provide that kind of info? Or I will need to write my own script for that?Again, since I have no direct MD-simulation experience, my understanding could be incomplete. If I guess it correctly, your MD simulations should include many snapshots. The output file for each parameter (e.g.,[mono:1b7xkmyt]x3dna_md_roll.out[/mono:1b7xkmyt] for Roll) from the Ruby scripts, [mono:1b7xkmyt]x3dna_md.rb/extract_par.rb[/mono:1b7xkmyt], contains tabulated values arranged in a m-by-n matrix, where m is the number of models/snapshots, and n is the number of base-pair steps. As noted in the initial release post, "The output parameter table is intended to be fed into R/Matlab/Octive/Excel etc for statistical analysis or visualization." Specially, I decided deliberately not to calculate mean/std etc statistics, even though it should be straightforward to add them.
I just tested the sample set and they seem to work fine.Thanks for being the first user to verify that the scripts are working as expected. I'd been expecting feedback from shahabshariati after I revised the scripts to v0.2 following his/her 'bug' report.
Instead of printing out model_1, model_2, etc.. We should just have the snapshot numbers, since an MD trajectory tends to have thousands of them.Do you mean to change the 1st column of each output parameter file from e.g., '[mono:1dzrze8o][red:1dzrze8o]model_10[/red:1dzrze8o][/mono:1dzrze8o]' to '[mono:1dzrze8o][red:1dzrze8o]10[/red:1dzrze8o][/mono:1dzrze8o]'? If that's the case, you can simply change line [mono:1dzrze8o]257[/mono:1dzrze8o] in function [mono:1dzrze8o]write_out_parameters()[/mono:1dzrze8o] of [mono:1dzrze8o]x3dna_md.rb[/mono:1dzrze8o] from
The stacking interactions are quantified in 3DNA by the shared overlap area, in Å2, of closely associated base rings, i.e. the nine‐membered ring of a purine R (A or G) and the six‐membered ring of a pyrimidine Y (C, T or U), projected in the mean base pair plane.So 3DNA, as is, may not provide a sensible value when a non-standard base ring is involved, such as your 3-ring linker. However, you can have a look of the corresponding step in the "stacking.pdb" file, and write a purpose-specific script to get your job done; after all, mathematically, it is all about getting the intersection of two polygons, and then calculating its area.
./x3dna_md.rb:94:in `each': no block given (LocalJumpError)You've helped me catch a 'potential' bug -- after googling for the error message, and checked the code, I believe I have fixed it.
pars[p] = parmtx.each.collect {|x| x[i]}
----->
pars[p] = parmtx.collect {|x| x[i]}The tricky part is that the error message did not show up in Ruby 1.9.2p0 on Ubuntu Linux (10.04) and 1.8.7 on Mac OS X Snow Leopard where I tested the scripts initially. Apparently, for the new versions of Ruby, [red:qc42htwt].each.collect[/red:qc42htwt] just introduces an extra loop over the list, which does no harm to the result. Put another way, you would not have noticed the 'bug' if you had used Ruby 1.8.7, or 1.9.x.I have just the template structure with the double strand sequence GCGT and I want, for example, to mutate the base pair CG with TA but I haven't found a similar example in the tutorial or in the examples.Conceivably, there are two ways to do what you want with 3DNA:
... the possibility of performing base mutations while keeping the backbone unchanged. Given this is such a common and clearly defined function, it is hard to imagine there is no such a handy standalone utility program from so many other resources to get the job done. Am I missing something here?I'd consider to write a script to automate the task, if there is still enough interest in this functionality and no other available tools are handy enough for this task.
As requested, an example of the DCD file (note that it is in binary format!) is attached along with a PDB template.Thank you so much for sharing a sample CHARMM DCD file, and providing an example to illustrate how to use it. Honestly, I am surprised that you did not forget my "request" –– if only more 3DNA users could be as generous and responsive! Active participations from enthusiastic users like you and Alpay certainly help make a difference.
The data was generated by running 1,000 steps of MD using implicit solvent.
I would be happy to share my experiences with using the MMTSB Tool Set.That would be great! In addition to Alpay's Python script (which I have moved to this section), my Ruby scripts, now users will have access to a Perl version of analyzing MD trajectories using 3DNA! Please start a new thread in this "Molecular dynamics simulations" section; and remember to provide a concrete example so that others can follow. I'd also be interested in seeing an sample DCD file.
See my post "Ruby scripts for the analysis of MD simulation trajectories". Please have your follow ups there.tar zxvf x3dna_md_v0.7.tar.gzand you will get a directory named x3dna_md_v0.7/, underneath you will find two Ruby scripts: x3dna_md.rb and extract_par.rb, and associated data files for testing and verification purpose.
----------------------------------------------------------------------
Usage:
x3dna_md.rb options
Examples:
x3dna_md.rb -b bpfile.dat -e sample_md0.pdb
# 21 models (0-21); output (default): 'x3dna_md.out'
# also generate 'model_list.dat', see below
x3dna_md.rb -b bpfile.dat -m model_list.dat -o x3dna_md2.out
# diff x3dna_md.out x3dna_md2.out
x3dna_md.rb -b bpfile.dat -p 'pdbdir/model_*.pdb' -o x3dna_md3.out
# note the quote for -p option; 20 models (1-20)
# also also generate 'pdb_list.dat', see below
x3dna_md.rb -b bpfile.dat -l pdb_list.dat -o x3dna_md4.out
# diff x3dna_md3.out x3dna_md4.out
# note the order of PDB files: 1, 10..19, 2, 20, 3..9
Options:
----------------------------------------------------------------------
--bpfile, -b <s>: File containing base-pairing info (as generated
from find_pair, and EDITED as appropriate)
--outfile, -o <s>: Output file name (default: x3dna_md.out)
--ensemble, -e <s>: Model ensemble in pairs
--models, -m <s>: Explicit list of model numbers
--pattern, -p <s>: Pattern of PDB files to process (e.g., *.pdb)
--list, -l <s>: Explicit list of individual PDB file
--version, -v: Print version and exit
--help, -h: Show this message
Note specifically that an input file with base-pairing (-b) information must be provided, which can be easily generated using find_pair and then manually edited as necessary. Needless to say, the base-pair file specified with -b must match the pairing configuration in each model of the ensemble. The input can be conveniently supplied with one of four options (-e, -m, -p, -l), allowing for great flexibility. Importantly, for the -e and -m options, each model in the ensemble must be delimited by an MODEL/ENDMDL pair, as clearly documented in the Coordinate Section of the PDB format.
----------------------------------------------------------------------
Usage:
extract_par.rb options
Examples:
extract_par.rb -l
# to see a list of all parameters
extract_par.rb -p prop
# -p 36 also fine (see above); from file 'x3dna_md.out'
# for propeller, no need to specify full: -p pr suffices
extract_par.rb -p slide -s , -f x3dna_md3.out
# comma separated, from file 'x3dna_md3.out', to screen
extract_par.rb -p roll -s ' ' -n > roll.dat
# space separated, no row-label, to file 'roll.dat'
extract_par.rb -a
# extract all parameters, each in a separate file
# prefixed with 'x3dna_md_': e.g., 'x3dna_md_chi1.out'
# run 'extract_par.rb -c' to clean up all generated files
extract_par.rb -e 1 -p chi1
# extract the chi torsion angle of strand I, but exclude
# those from the two terminal base pairs. For comparison,
# run also: extract_par.rb -p chi1
Options:
----------------------------------------------------------------------
--no-1col, -n: Delete the first annotation column
--separator, -s <s>: Separator for fields [tab] (default: )
--list, -l: List all parameters
--all, -a: Extract all parameters into separate files
--clean, -c: Clean up parameter files by the above -a option
--par-name, -p <s>: Name of parameter
--fromfile, -f <s>: File name with parameters (default:
x3dna_md.out)
--end-effects, -e : No. of end pairs to ignore (default: 0, 0)
--version, -v: Print version and exit
--help, -h: Show this message
Three sample output files are attached below for reference: propeller.tsv contains propeller of 21 models of a 12-mer in the default tab-delimted format; slide.csv contains roll in comma separated format; and roll.dat in space separated format, without leading label column. The output parameter table is intended to be fed into R/Matlab/Octive/Excel etc for statistical analysis or visualization.Thanks for the note re the w3DNA server. The BioMaPS staff, which we have contacted, has been helping with the website since Guohui left. Sometimes the site overflows with extraneous data and is then relaunched.Moreover, Dr. Olson has asked Andrew Colasanti to help with w3DNA-related issues.
They are stored in 100 seperate PDBs.Is this norm? I cannot imagine that a MD simulation with thousands of snapshots ends up with thousands of PDB files. Anyway, are your 100 PDBs all stored in a directory? Do the PDB files share a specific pattern?
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