Messages

1351

MD simulations / Re: Ruby scripts for the analysis of MD simulation trajector

« on: March 05, 2011, 07:23:40 pm »

Hi Alpay,

As always, thanks for your feedback and suggestions. Now specifically,

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.

Download v0.3 to have a try, and report back any issues you experience; and of course, any new suggestions!

Xiang-Jun

1352

MD simulations / Re: average values from MD simulations

« on: February 28, 2011, 12:13:19 am »

Hi Ara,

Thanks for using 3DNA, and for posting your question(s) in the forum. I am glad to hear that you found the Ruby scripts useful to your analysis of drug-DNA MD simulations -- at the very least, I take it as yet another user confirmation that the Ruby scripts are working as expected.

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.

On the other hand, the files "bp_helical.par" and "bp_step.par" are from each run of the [mono:1b7xkmyt][red:1b7xkmyt]analyze[/red:1b7xkmyt][/mono:1b7xkmyt] program on a snapshot, i.e., they are from native 3DNA output, and are overwritten each time unless you renamed them. Put another way, these two files are not related to your MD analysis; instead they are intended to be used with the [mono:1b7xkmyt][red:1b7xkmyt]rebuild[/red:1b7xkmyt][/mono:1b7xkmyt] program to construct DNA structures as specified by the parameters.

HTH,

Xiang-Jun

1353

MD simulations / Re: Ruby scripts for the analysis of MD simulation trajector

« on: February 23, 2011, 08:43:14 pm »

Hi Alpay,

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.

I added the [mono:1dzrze8o]-all[/mono:1dzrze8o] option simply because it makes sense to me. As mentioned previously, I have no MD experience. Nevertheless, I am glad to know that this functionality coincides with Curves.

Regarding the next step, what do you mean exactly "to incorporate some distribution calculation"? Some simple statistics, maybe?

Regarding your comment/suggestion,

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
[pre:1dzrze8o]c0 = "model_#{entries[idx]}"[/pre:1dzrze8o]to [pre:1dzrze8o]c0 = entries[idx][/pre:1dzrze8o]
Thanks for your feedback. Please clarify so I can improve the scripts.

Xiang-Jun

1354

General discussions (Q&As) / Re: overlap area of stacked linkers

« on: February 14, 2011, 09:02:50 pm »

As mentioned in the 2003 3DNA NAR paper:

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.

If you want to go further along the line with 3DNA, please make your problem specific. By using your case as an example, we may extend 3DNA, or at least provide a use-case, in ways potentially useful to other users.

Xiang-Jun

1355

MD simulations / Re: Ruby scripts / where is output file?

« on: February 12, 2011, 11:57:21 am »

./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.

Just for the record, here is an example where the change has been made: ([red:qc42htwt].each.collect[/red:qc42htwt] to [red:qc42htwt].collect[/red:qc42htwt])

Code: [Select]

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.

Download and reinstall the revised script v0.2, and report back what you get; I will be surprised if you still have the same problem  :oops:

As always, I welcome bug reports -- the more, the merrier!

Xiang-Jun

1356

General discussions (Q&As) / Re: Problems with mutations on DNA

« on: February 11, 2011, 08:52:03 pm »

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:

• Use the "[mono:2j91smsb]analyze/rebuild[/mono:2j91smsb]" pair, as follows (assuming your PDB file is named [mono:2j91smsb]sample.pdb[/mono:2j91smsb]):
  [pre:2j91smsb]find_pair sample.pdb stdout | analyze
  [red:2j91smsb]# In addition to sample.out file, the above will also generate a text file named "bp_step.par".
  # Manually edit it as you see fit, e.g., change a C-G pair to T-A, and name it "new_step.par"[/red:2j91smsb]
  rebuild -atomic new_step.par sample_new.pdb
  [red:2j91smsb]# Refer to FAQ #5 if you want to build a structure with sugar-phosphate backbone.[/red:2j91smsb][/pre:2j91smsb]
  If you have many mutations to perform, it should be straightforward to write a script to automate the process. The possible issue with this approach is that the sugar-phosphate backbone conformation is approximate, and will certainly be different from what you start with.
  
• For a more general approach where the backbone is kept untouched, see the thread "mutating DNA in DNA protein complex". The problem here is that the procedure is not automated (yet). Three years later, I still have the same question:
  

  ... 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.

Alternatively, another tool you could try is mutateNA.pl within MMTSB.

HTH, and I hope to see your feedback.

Xiang-Jun
(added June 5, 2011):
Please see the thread "change one base pair in a double-strand DNA structure file"
where the Perl script mutate_bp and the ANSI C program mutate_bases are introduced.

1357

MD simulations / Re: 3dna.pl - A Perl Script for Parsing 3DNA Output

« on: February 10, 2011, 10:29:25 pm »

As requested, an example of the DCD file (note that it is in binary format!) is attached along with a PDB template.

The data was generated by running 1,000 steps of MD using implicit solvent.

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.

Xiang-Jun

1358

MD simulations / Re: Ruby scripts / where is output file?

« on: February 10, 2011, 10:19:44 pm »

Thanks for trying out the Ruby scripts for MD trajectories  analysis with 3DNA. To help debug the problems you experienced, please try the following:

• What version of Ruby you have? i.e., what "[red:2pf22pld]ruby -v[/red:2pf22pld]" outputs? Which OS are you using?
• What happens if you run the sample dataset distributed with the Ruby scripts? i.e., in the installed directory, run:
  [pre:2pf22pld][red:2pf22pld]./x3dna_md.rb -b bpfile.dat -e sample_md0.pdb[/red:2pf22pld][/pre:2pf22pld]Does it work, or give any error message?
• Please attach your PDB file, so others can reproduce your problem.

Xiang-Jun

1359

MD simulations / Re: the sign of minor or major groove width

« on: February 10, 2011, 10:06:26 pm »

Well, I can only help with 3DNA. As I said in my previous post, all groove dimensions from 3DNA are positive.

To be specific with any further discussion on this thread, please provide a PDB file (possibly with a picture as well) which has "negative" groove width.

HTH,

Xiang-Jun

1360

MD simulations / Re: the sign of minor or major groove width

« on: February 09, 2011, 07:42:58 pm »

3DNA calculates minor and major groove widths, following El Hassan and Calladine:

[pre:4yesx38r]Minor and major groove widths: direct P-P distances and refined P-P distances
   which take into account the directions of the sugar-phosphate backbones

   (Subtract 5.8 Angstrom from the values to take account of the vdw radii
    of the phosphate groups, and for comparison with FreeHelix and Curves.)

Ref: M. A. El Hassan and C. R. Calladine (1998). ``Two Distinct Modes of                          
     Protein-induced Bending in DNA.'' J. Mol. Biol., v282, pp331-343.[/pre:4yesx38r]
By definition, the groove widths output from 3DNA should be positive.

HTH,

Xiang-Jun

1361

MD simulations / Re: 3dna.pl - A Perl Script for Parsing 3DNA Output

« on: February 03, 2011, 11:47:12 pm »

Hi Sean,

Thanks for contributing your Perl script for parsing 3DNA output! I've downloaded and played around with it a bit, and found it well-formatted and documented. I am impressed that your script parses 3DNA output in such a flexible way, and integrates nicely with the MMTSB Tool Set for handling MD simulation trajectories. Well-done!

I am sure the 3DNA user community will benefit from your effort; I am hopefully more would follow your lead to share their scripts or experiences.

Xiang-Jun

1362

MD simulations / Re: Ruby scripts for the analysis of MD simulation trajector

« on: January 31, 2011, 07:33:45 pm »

Hi Sean,

Thanks for sharing the info -- I came across MMTSB before, but did not get a chance to play with it. This is the first time I hear of the binary DCD trajectory files produced by CHARMM/NAMD. The Perl script "processDCD.pl" seems useful, too. I've downloaded MMTSB, and would like to spend some time to it.

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.

Best regards,

Xiang-Jun

1363

General discussions (Q&As) / Re: script for extracting data from 3DNA output file

« on: January 19, 2011, 12:16:10 am »

Hi Aneesh,

Finally, I've come up with something to present    See my post "Ruby scripts for the analysis of MD simulation trajectories". Please have your follow ups there.

Cheers!

Xiang-Jun

1364

MD simulations / Ruby scripts for the analysis of MD simulation trajectories

« on: January 19, 2011, 12:11:44 am »

Hi MD practitioners,

Here is the updated release v0.7 of two Ruby scripts that aim to streamline the analysis of MD simulation trajectories with 3DNA. There is also a blog post with more background information, but here are the most relevant:

• Where to download http://3dna.rutgers.edu:8080/data/x3dna_md_v0.7.tar.gz
• How to install (see README file for more information):

  tar zxvf x3dna_md_v0.7.tar.gz

  and 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.
• How to run x3dna_md.rb: this script needs to be run first. Detailed help message (with -h) is shown below:
  

  ----------------------------------------------------------------------
  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.
  
  The output file contains a comprehensive set of 3DNA calculated parameters, each enclosed in an xml-style tag pair; e.g., <propeller>...</propeller>. Each parameter is arranged in a tab-delimited m-by-n matrix, where m is the number of models, and n is the number of base-pairs or steps. The default file name is x3dna_md.out and an example is attached.
• How to run extract_par.rb: this script needs to be run after x3dna_md.rb. Detailed help message (with -h) is shown below:
  

  ----------------------------------------------------------------------
  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.
• Acknowledgments: thanks to Aneesh for the final "push"; Alpay for sharing his Python script, and providing an example data set on which the Ruby scripts were tested.
  
  The Ruby scripts takes advantage of William Morgan's Trollop (v1.16.2) (http://trollop.rubyforge.org/) for command line option parsing. To make the scripts self-contained, the single file trollop.rb is included with the distribution.
  
  The scripts were tested with Ruby 1.9.2p0 on Ubuntu Linux (10.04), and 1.8.7 on Mac OS X Snow Leopard.

Enjoy, and do not forget to report back any problems you experience!

Version history

• 2011-01-18: v0.1, first release.
• 2011-02-12: v0.2, fixed a bug with `each': no block given -- thanks to shahabshariati!
• 2011-03-05: v0.3, removed the model_ prefix at the first column of extracted parameter file; added the -e option to delete parameters associated with terminal base-pairs -- thanks to Alpay's suggestions.
• 2011-03-16: v0.4, significant refinement of the scripts (in line of defensive programming) to check for various possible erroneous inputs (e.g., mismatched base-pair file, ensemble not delimited by MODEL/ENDMDL pairs etc); added -d option to make error message more obvious; added a comprehensive README file.
• 2011-04-02: v0.5, added return value checking of system() calls, plus other refinements.
• 2011-05-29: v0.6, refined system-call and pair checking with more informative message.
• 2011-09-30: v0.7, added H-bond and overlap areas parameters, and the -c option in extract_par.rb.

Xiang-Jun

1365

w3DNA -- web interface to 3DNA / Re: Problem connecting to w3DNA server

« on: January 11, 2011, 11:31:10 pm »

Hi Eugene,

Thanks for reporting the issue you experienced with access to w3DNA. I communicated with Dr. Olson, and here is her reply:

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.

I've checked w3DNA, which seems to be functioning properly. If you have any further problem, please report back.

Thanks,

Xiang-Jun

1366

MD simulations / Re: A modified 3DNA parser for MD trajectory analysis

« on: January 07, 2011, 09:30:39 pm »

Hi Alpay,

Thanks for your contribution! Hopefully, more 3DNA users would share their experiences through the forum.

Xiang-Jun

1367

General discussions (Q&As) / Re: script for extracting data from 3DNA output file

« on: January 07, 2011, 09:26:28 pm »

Hi Aneesh,

In addition to Alpay's above reply, did you also notice his most recent post "A modified 3DNA parser for MD trajectory analysis" at the section of Users' contributions. Please have a try and report back your experience.

I will try to come up with a script that hopefully streamlines the process of extracting 3DNA output from MD trajectory analysis. Alpay's parser may well serve as a starting point.

HTH,

Xiang-Jun

1368

General discussions (Q&As) / Re: script for extracting data from 3DNA output file

« on: January 06, 2011, 10:12:29 pm »

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?

Additionally, are you familiar with R or Matlab/Octave? In my mind, the script to extract 3DNA output parameters would ideally write a tab-delimted data table that can be easily fed into commonly available tools for easy calculation of mean/std etc statistics.

I am pretty occupied with my job right now, but I will try to "spare" some time to come up with a preliminary script to get you started (hopefully by the end of next week).

Xiang-Jun

1369

General discussions (Q&As) / Re: script for extracting data from 3DNA output file

« on: January 04, 2011, 09:47:06 pm »

Welcome back. It is certainly clearer than before. However, it would be far more helpful if you could be even more specific, i.e., by providing an example. For example, I am not sure what the "100 snapshots (PDBs) from the simulation trajectories" look like. Are the 100 snapshots stored in 100 separate PDB files, or all in one? If the later, how are the snapshots separated? By MODEL/ENDMDL as in NMR structure? What would be an appropriate output format for the extracted parameters? In addition to the mean values of some parameters, e.g., Twist, how about their standard deviations and other related simple statistics? All such details need to be considered to come up with a script that is more generally applicable.

Thus, to help others help you more effectively, try to come up with a (minimum) concrete example, including all necessary input data files and your expected results (in numbers). Moreover, if you have already written some scripts, attach them with your post.

Alternatively, as mentioned in my blog post "Curves+ vs 3DNA", Curves+ has built in support for the analysis of MD simulation trajectories, and it may well serve your need.

HTH,

Xiang-Jun

1370

General discussions (Q&As) / Re: script for extracting data from 3DNA output file

« on: December 25, 2010, 10:44:26 pm »

Hi Aneesh,

Over the years, I have written a few posts related to the topic of applying 3DNA to the analysis of molecular dynamics (MD) simulations, including:

• 3DNA for the analysis of molecular dynamics simulations
• 3DNA in molecular dynamics simulations
• Curves+ vs 3DNA

Also, I contacted a couple of practitioners in the MD field, trying to seek a possible collaborator to make using 3DNA more straightforward for this increasing user community. For various reasons, nothing significant has come out from this effort. I am hoping users who have successfully applied 3DNA in MD analysis would contribute their scripts so others can benefit from and build upon. In the meantime, if you could post your MD analysis procedure and the problems you faced, others (myself included) may be able to help you more concretely.

Xiang-Jun

1371

General discussions (Q&As) / Re: window 7

« on: December 15, 2010, 09:09:23 pm »

Thanks for using 3DNA in Windows!

Which version of 3DNA are you referring to? If you are still using v1.5, it is definitely time to upgrade to v2.0. There are two 3DNA v2.0 binaries for Windows:

• Cygwin on Windows (see Cygwin homepage for details)
• Native Windows binaries with MinGW (see MinGW homepage for details; you may also want to have MSYS installed)

I am not a regular Windows user, but I did not meet much problem to compile 3DNA on a Windows XP machine in the two environments. I guess they should run on Windows 7, if you install either Cygwin or MinGW/MSYS -- you are the first to report such a problem of installing 3DNA on Windows. Please have a try and report back how it goes.

Any comments from other Windows users?

HTH,

Xiang-Jun

1372

General discussions (Q&As) / Re: Single strand DNA

« on: December 15, 2010, 08:52:10 pm »

I am not sure I understand the question. 3DNA does not perform any structure validation; it simply calculates some geometrical parameters given a structure (including single stranded DNA) in PDB format. As far as (NMR) structure validation goes, have a look of CING, or MolProbity.

HTH,

Xiang-Jun

1373

General discussions (Q&As) / Re: Missing Groove Measurement

« on: December 08, 2010, 09:07:26 pm »

Hi, Sean:

Hopefully the blog post you referred to, "3DNA for the analysis of molecular dynamics simulations", helps solve your problem. If any thing is still unclear, please provide a concrete example case.

Xiang-Jun

1374

General discussions (Q&As) / Re: O1P_O2P program

« on: November 15, 2010, 07:42:00 pm »

Hi Pascal,

Thanks for reading my recent blog post on O1P/O2P labeling, which was inspired by your above question!

given the recent PDB changes, is the O1P_O2P still interesting to use? Yet, after checking some of them, I noted that these changes occur mostly for terminal residues and I am not sure that everything is OK at this level (you could eventually like to check file 10MH).

The mislabeling issue should not have happened in PDB/NDB in the first place. The very fact that such error did happen, as shown for [mono:3dv13ht8]adh026[/mono:3dv13ht8], prompted the creation of the [mono:3dv13ht8]o1p_o2p[/mono:3dv13ht8] utility program. I am not surprised at all if you still find mislabeled O1P/O2P atoms in the currently "remediated" PDB files. I have quickly checked [mono:3dv13ht8]10MH[/mono:3dv13ht8] --  the two terminal phosphate groups (DC-402  on chain B and DG-422  on chain C) apparently still have O1P/O2P mislabeled.

On my side, I will continue to check the files, it might well be that some modified residues are also mislabeled in original files.

I think it is certainly a good idea to continue to check the files you care about. The command-line driven [mono:3dv13ht8]o1p_o2p[/mono:3dv13ht8] utility can be applied to any compliant PDB file, not just the one from PDB/NDB. Please report back if meet further issues, or have a request for added functionality :wink:.  Hopefully, I'd be able to "spare" more time to address 3DNA-related questions in the future   .

Xiang-Jun

1375

General discussions (Q&As) / Re: O1P_O2P program

« on: November 08, 2010, 10:24:15 pm »

Hi Pascal,

First, some background information: the utility program [mono:2uhtgbv8]o1p_o2p[/mono:2uhtgbv8] was written for a simple, specific purpose: long time ago, while calculating the RMSD value between the A-DNA NDB entry [mono:2uhtgbv8]adh026[/mono:2uhtgbv8] and the corresponding 3DNA rebuilt structure (with sugar-phosphate backbone), I noticed this RMSD was much larger than expected. Further inspection revealed that the issue was due to a mislabeling of O1P and O2P atoms for this specific NDB entry at that time (still available in directory [mono:2uhtgbv8]X3DNA/examples/analyze_rebuild[/mono:2uhtgbv8]). So [mono:2uhtgbv8]o1p_o2p[/mono:2uhtgbv8] was designed to check for proper O1P/O2P labeling, and to swap them if necessary, given a PDB file. Overall, the utility program works for its purpose, and has been released as part of 3DNA from the very beginning.

As a side note, current PDB/NDB entries have changed O1P/O2P to OP1/OP2. The mislabeling of O1P/O2P for [mono:2uhtgbv8]adh026[/mono:2uhtgbv8] has been corrected. Also, 3DNA v2.0 identifies OP1/OP2 labeling internally, but I still prefer to use O1P/O2P in 3DNA output.

[hr:2uhtgbv8][/hr:2uhtgbv8]
Now back to your question: I am glad that you've found [mono:2uhtgbv8]o1p_o2p[/mono:2uhtgbv8] useful. I know the problem you refer to, regarding header removal from [mono:2uhtgbv8]o1p_o2p[/mono:2uhtgbv8] output PDB file. However, current version of [mono:2uhtgbv8]o1p_o2p[/mono:2uhtgbv8] does not have an option to keep header as is. Conceivably, it should be feasible to add such functionality. I'll consider to put this point in my to-do list for future release of 3DNA (I am busy for my job until the following couple of weeks   ). In the meantime, you may prefer to write a script to extract the header from original PDB file, combined with "corrected" O1P/O2P coordinates.

HTH,

Xiang-Jun