Messages

1401

Feature requests / Re: Align multi-model (NMR) structures

« on: December 28, 2011, 09:09:44 pm »

Hi Andrew,

Thanks for this feature request and for providing two sample images -- it would indeed make a nice feature for future release of 3DNA. There are many things I would like to consolidate/refine, and new features to add! This requested feature fits nicely to the overall scheme I have in mind.

Before I can get something for an "official" release of 3DNA v2.1 with this new feature included, I will try to come up with a Ruby script this week for you to try out.

Now to a specific point related to the procedure your outlined:

I have a suggestion on a new feature for multi-model NMR files, some sort of alignment command to align on each model's reference frame.  I performed this by hand as an example using the following

- Split the multi-model file into individual pdb files, 1 for each model
- for each model...
  - find_pair on the structure
  - rotate_mol using the ref_frame.dat file from find_pair

The pairing is consistent in all of the models but we have to run find_pair on each structure in order to get the reference frame data.

As with the MD simulation analysis script ('x3dna_md.rb'), it would be best for a user to specify the base pairing information. Thus the program 'find_pair' does not need to be run with each model. This would ensure consistency in all the models. Instead, the model-specific 'ref_frame.dat' can be generated with 'analyze'.

Check back ...

Xiang-Jun

1402

General discussions (Q&As) / Re: std_curved parameters seems not to work in 3DNA V2.1

« on: December 01, 2011, 11:25:51 am »

I certainly should have made such cases more explicit -- I will add a new section to the forum, titled "Bug reports and feature requests", by the end of the week. As I am working on improving 3DNA, do you have any desired features or suggestions to make the software more useful? Do not be shy!

Xiang-Jun

1403

General discussions (Q&As) / Re: std_curved parameters seems not to work in 3DNA V2.1

« on: December 01, 2011, 06:53:11 am »

Greetings Mauricio!

It was (still is) a bug, but see thread "Global Helical Axis Information Missing". It's well worths repeating that for a word-around (for the time being), please do the following:

Code: [Select]

<std_curved >0.6</std_curved >   # add a space in the end of the tag!Just to clarify, [red:298epu6t][mono:298epu6t]3DNA v2.0 [August 2007][/mono:298epu6t][/red:298epu6t] was a pre-release for testing of v2.0 (beta) before the 2008 3DNA Nature Protocols paper was published; [red:298epu6t][mono:298epu6t]3DNA v2.0 [June 8, 2008][/mono:298epu6t][/red:298epu6t] is the currently distributed version. 3DNA [red:298epu6t]v2.1[/red:298epu6t] is not out yet, but I am planning to release it in the near future -- by early next year!

Thanks for reporting the bug! As always, the more bug reports, the merrier!

Xiang-Jun

1404

General discussions (Q&As) / Re: PNA-DNA duplex study using 3DNA

« on: November 26, 2011, 10:06:26 am »

Hi SOUVIK,

Thanks for using 3DNA, and posting your question at the forum.

Your attached sample PDB file 'nspP.pdb' helped me trace the origin of the problem. As shown in the chemical structure of residue K19 in your PNA-DNA complex, its atomic naming clearly does not following the PDB convention for A (purine). See my blog post "PDB ATOM coordinates record". Thus the residue is not taken as a nucleotide by 3DNA (try: find_pair -s nspP.pdb stdout) to begin with, no wonder "no basepairs found".

To solve your problem, it is best to start from the source, i.e., the software (AMBER) which generates the PDB file. Alternatively, you can write a purpose-specific script to change the base names of each PNA residue following PDB naming convention for DNA/RNA. Thirdly, if there are enough interest and use cases, I may consider adapt or create such a converting script to be distributed with future releases of 3DNA.

HTH,

Xiang-Jun

1405

General discussions (Q&As) / Re: modelling ssDNA or ssRNA

« on: November 17, 2011, 07:38:23 am »

Hi Laura,

Thanks for your interest in 3DNA and for posting on the forum.

I understand what you mean, but I do not think 3DNA (or other tools I know of) can provide you with a straight answer. It all depends -- what specifically is your definition of "an extended conformation", i.e., "single strands without helical configurations"? If you have a starting model, mutate_bases and analyze/rebuild/frame_mol in 3DNA may help.

As always, I am willing to extend 3DNA in ways that make sense to me and are useful to the community. Currently, 3-dimensional nucleic acid structure modeling is one aspect I am interested in.

Xiang-Jun

1406

General discussions (Q&As) / Re: DNA Triple Helix Generation

« on: October 22, 2011, 09:46:05 am »

Hi Himanshu,

I know English is not my native language, but do you really have any problem in understanding my previous two replies to your questions in the thread?

I wish 3DNA could be helpful to your project. However, 3DNA has been designed for some specific purposes, and apparently it does not fit your need. Please check some other (docking) software, e.g., HADDOCK from Alexandre Bonvin. Good luck!

Xiang-Jun

1407

General discussions (Q&As) / Re: DNA Triple Helix Generation

« on: October 21, 2011, 07:18:38 am »

Hi Himanshu,

Fig1.png(as attachment) : ... green ribbon shows single strand DNA which is ligand to dock in double stranded DNA. In the green ribbon there is intra-molecular bonding.

Thanks for attaching a PNG image illustrating the unusual "intramolecular bonding(backbone and nitrogen bases)". It is certainly clearer than pure text description. However, it would be even better if you provide the corresponding PDB file so others can easily visualize the problematic structure.

Can we ignore those bonds?

I do not know how you generated the structure, and for what purpose, thus I cannot offer any advice in this regard. The question appears not to be directly 3DNA-related. However, the image does show that the ssDNA is in poor geometry.

Xiang-Jun

1408

General discussions (Q&As) / Re: DNA Triple Helix Generation

« on: October 20, 2011, 07:01:55 am »

Hi Himanshu,

Thanks for posting at the 3DNA forum. Just to be clear, 3DNA does not perform DNA-DNA docking or any energy calculations.

But, the ssDNA show intramolecular bonding(backbone and nitrogen bases) which is un-usual.

Could you elaborate on it? Better with a specific example.

However, 3DNA does provide the following approach for DNA triplex creation which may be useful to your project:

• Build a fiber model (e.g., #31) for Poly (U) : poly (A) : poly(U) (11-fold). Type "[mono:26cqmn7j]fiber -m[/mono:26cqmn7j]" for more info, and search the forum for related posts. Alternatively (or better), pick a related triplex structure from the PDB, or another source.
  
• Perform base mutations (using [mono:26cqmn7j][red:26cqmn7j]mutate_bases[/red:26cqmn7j][/mono:26cqmn7j]) to your specific sequence. See thread "change one base pair in a double-strand DNA structure file".

Please note that the mutated triplexes may have steric clashes (atoms too close) or longer than ideal H-bonding geometry: they are intended as initial structures for refinement using any of the available energy calculation tools.

HTH,

Xiang-Jun

1409

General discussions (Q&As) / Re: 3DNA on 64 bit Linux (Ubuntu)

« on: October 19, 2011, 12:59:01 pm »

I have a problem with running 3DNA on 64 bit Fedora. It says "can't execute the binary file" whenever I try to run any of the programs from 3DNA/bin directory. The PATH and X3DNA environmental variables are set correctly.
Is there a version of 3DNA for 64 bit Linux systems available?

Glad to know the detailed error message. With two cases, now it seems clear that the 32 bit version of 3DNA compiled in Ubuntu does not work in 64 bit machines.

Check email for download info of a 64-bit compiled version of 3DNA and report back if it work on your 64 bit Fedora.

Thanks for using 3DNA and posting in the forum.

Xiang-Jun

1410

MD simulations / Re: H-bonding information in MD analysis output

« on: October 04, 2011, 07:25:42 am »

Hi Andre,

I will try to work with the extract output and organise the data as you suggested. I guess I'm trying to make it easier to see the type of H-bond events that are occuring.

It makes sense. Over the years, 3DNA has been used in ways that are out of my original intention. As a principle, I won't add a 'feature' into 3DNA unless I fully understand it and can back it up when asked. Put another ways, feature-rich is not what 3DNA aims for, but quality is. This is where purpose-specific scripting comes into play, and such a skill is essential for a 'bioinformatican'.

I am not experienced in programing/scripting so it will be an interesting challenge. I'll post the script here if I'm successful as others may have a use for it.

We all learn from practice, and by making mistakes. I am willing to help you in the exercise: just put your script with a reproducible example here, then I (hopefully other viewers of the forum) can make suggestions. With several iterations, the problem will become clearer, and your script may well function for your needs. In retrospect, this is the most effective way to learn things, and I wish to have been guided this way. I aim to turn this forum into a 'educational' resource so that people with similar mind can share and benefit from each other's experience and contributions. I am glad that you are willing to share, which is precisely the incentive that I'd like to help you more.

Have a try, and let's see how it goes.

Xiang-Jun

1411

MD simulations / Re: H-bonding information in MD analysis output

« on: October 03, 2011, 10:19:00 pm »

Hi Andre,

This may be a process that the extract script will have to handle after 'analyze'.

As mentioned previously, I am not convinced to add such a functionality directly in the current two Ruby scripts. If you want to proceed, it is preferable (in my understanding) to start from the extracted [mono:13mhwi7u]<hbond>[/mono:13mhwi7u] parameters. A purpose-specific script is the way to go.

Let's use wastson crick pairing as our conventional H-bond information. For your GC pair example, can we extract and organsie the information so the first column is O2 - N2, second is N3 - N1, and the third is N4 - O6. If there are non-waston crick H-bonds they can be placed in the fourth and subsequent columns.

In addition to G-C pair, you also need to consider C-G pair, which by default swaps the order of atoms in H-bond output.

Do we have to specify all the non-waston crick H-bonds or can the script look for the waston crick H-bonds and place the non-waston crick H-bonds after the standard waston crick information?

It is entirely up to you, with a purpose-specific script.

HTH,

Xiang-Jun

1412

MD simulations / Re: H-bonding information in MD analysis output

« on: October 02, 2011, 09:40:40 am »

Since the H-bond information for each base pair is arranged in columns, is there a way for the script to define each column for a specific H-bond and if the bond does not exist then it will leave it blank?

The parsing script has no knowledge of any 'specific H-bond': it just takes H-bonds for each base-pair as a single unit of text string. The H-bond info is calculated with 'analyze', based on purely geometric criteria. Thus for example there can be different A-T pairs: e.g., Watson-Crick pair and Hoogsteen pair, and many other possibilities.

In the example shown in my first reply, note the first two C-G pairs:

1 C-----G  [2]  O2 - N1  2.99  N4 - O6  2.98
2 C-----G  [3]  O2 - N2  2.74  N3 - N1  2.84  N4 - O6  3.17

They are based on model #20 of the distributed PDB ensemble 'sample_md0.pdb'. Note specifically, while the 2nd C-G pair is normal with 3 H-bonds, the first C-G pair has 2 H-bonds including the unconventional 'O2 - N1  2.99'.

Overall, I cannot see a sensible, generally applicable way to "define each column for a specific H-bond".

Here is a file to show you what I mean

I realise this is just formatting however it will make life easier to have the script format the output rather than do it manually.

See above. For your example, the first column does not align. Think about all the possible base sequence and pairing patterns, what you are asking for is certainly not just a formatting matter.

0   [3]   O2 - N2   2.96   N3 - N1   3.03   N4 - O6   3.49
1   [3]   O2 - N2   3.53   N3 - N1   2.97   N4 - O6   2.75
2   [3]   O2 - N2   3.01   N3 - N1   2.78   N4 - O6   3.19
3   [3]   O2 - N2   3.17   N3 - N1   3.25   N4 - O6   3.53
4   [3]   O2 - N2   2.81   N3 - N1   2.97   N4 - O6   3.22
5   [3]   O2 - N2   2.86   N3 - N1   2.87   N4 - O6   2.86
6   [1]         N3 - N1   3.08      
7   [2]         N3 - N1   3.25   N4 - O6   2.78
8   [2]   O2 - N1   3.07         N4 - O6   3.35
9   [3]   O2 - N2   2.96   N3 - N1   2.71   N4 - O6   2.85
10   [3]   O2 - N2   3.32   N3 - N1   2.87   N4 - O6   3.09
11   [3]   O2 - N2   3   N3 - N1   2.86   N4 - O6   3.18
12   [2]         N3 - N1   3.14   N4 - O6   3.04
13   [2]   O2 - N2   2.75   N3 - N1   3.29      
14   [3]   O2 - N2   3.04   N3 - N1   3.06   N4 - O6   3.38
15   [3]   O2 - N2   2.85   N3 - N1   2.99   N4 - O6   3.21
16   [3]   O2 - N2   3.17   N3 - N1   2.93   N4 - O6   2.98      
17   [3]   O2 - N2   2.79   N3 - N1   2.74   N4 - O6   2.6      
18   [3]   O2 - N2   3.03   N3 - N1   2.78   N4 - O6   2.66      
19   [2]   O2 - N1   2.75               N3 * O6   3.32
20   [2]   O2 - N1   2.99         N4 - O6   2.98

I understand you may have a clearly defined goal in hand, and that's where application-specific scripting/programming comes into play. I may be able to help in some way if you make your case more specific.

Xiang-Jun

1413

MD simulations / Re: H-bonding information in MD analysis output

« on: September 30, 2011, 10:17:44 am »

Hi Andre,

Please check the updated post "Ruby scripts for the analysis of MD simulation trajectories". Now in v0.7, the scripts parse and extract H-bonding information you asked for, and also the overlap areas for quantifying stacking interactions.

Now I realized that I had a (solid) reason to exclude H-bond parameters in the scripts -- being variable-length text instead of float numbers (see my first reply in this thread for an example), they do not fit the pattern with other previously extracted parameters. Specifically, with N models (structures) and each M base-pairs, we have a N-by-M data matrix for each of the base-pair parameters.  For buckle, see the attached file 'buckle.tsv' (based on the distributed dataset [mono:kldkpnjg]sample_md0.pdb[/mono:kldkpnjg]. Here '[mono:kldkpnjg]tsv[/mono:kldkpnjg]' stands for tab-separated values). Now for H-bonding, the extracted data file 'hbond.tsv' looks a bit wildly -- each item has different text length and number of H-bonds. I cannot see how such information can be processed directly as with other parameters, and I'd be interested in knowing how you proceed.

Have a try, and see how it goes.

Xiang-Jun

1414

MD simulations / Re: H-bonding information in MD analysis output

« on: September 29, 2011, 07:03:12 am »

Hi Andre,

Thanks for your feedback. I will add a section of H-bond parameters (hopefully) by tomorrow, and then release an updated version of the Ruby scripts. So stay tuned, and check back the forum.

Xiang-Jun

1415

MD simulations / Re: H-bonding information in MD analysis output

« on: September 28, 2011, 07:17:37 am »

Hi Andre,

First, thanks for posting your question in the forum! The more user feedback, the merrier.

Second, you may notice that I have split your post from the thread "Ruby scripts for the analysis of MD simulation trajectories" which is too long (18 posts now), and spans two pages.  I have added a new subject line "Re: H-bonding information in MD analysis output" for the new thread.

Third, and more relevant to your question, are you referring to adding a new section for the H-bonding information? An example would be:

<hbond>
   1 C-----G  [2]  O2 - N1  2.99  N4 - O6  2.98
   2 C-----G  [3]  O2 - N2  2.74  N3 - N1  2.84  N4 - O6  3.17
   3 T-----A  [2]  N3 - N1  3.09  O4 - N6  2.86
   4 A-----T  [2]  N1 - N3  2.78  N6 - O4  3.05
   5 A-----T  [2]  N1 - N3  2.81  N6 - O4  2.76
   6 T-----A  [2]  N3 - N1  2.71  O4 - N6  3.06
   7 A-----T  [2]  N1 - N3  3.12  N6 - O4  3.12
   8 G-----C  [2]  N1 - N3  3.00  O6 - N4  2.75
   9 A-----T  [2]  N1 - N3  2.93  N6 - O4  3.12
  10 A-----T  [2]  N1 - N3  2.90  N6 - O4  2.93
  11 A-----T  [2]  N1 - N3  3.01  N6 - O4  3.05
  12 T-----A  [2]  N3 - N1  2.80  O4 - N6  3.12
</hbond>

If that's the case, then it won't be much a problem to parse and add it into the output file. Otherwise, please provide a concrete example to show exactly what you mean.

Please confirm.

Xiang-Jun

1416

General discussions (Q&As) / Re: constructing a modified sugar

« on: September 12, 2011, 08:21:52 am »

...i am successful in making the modification using chimera software which has a menu called 'Build structure'. It would be nice to have this feature incorporated in 3DNA.

Glad to hear that you are successful in making sugar modification with Chimera 'Build structure'. If that does a decent job, why should 3DNA bother to compete (recreating the wheel)? That's exactly why I asked you the question in my preview reply.

Xiang-Jun

1417

General discussions (Q&As) / Re: 3DNA on 64 bit Linux (Ubuntu)

« on: September 09, 2011, 11:19:58 pm »

Hi Fei,

I did not realize 3DNA v2.0 compiled in 32-bit Ubuntu Linux does work in a 64-bit machine. Yours is the first reported case. Any comment / experience from other users?

Anyway, check email for download link to 3DNA v2.0 compiled in Scientific Linux 6 x86_64. Do report back here if it works, or not.

Xiang-Jun

1418

General discussions (Q&As) / Re: constructing a modified sugar

« on: September 08, 2011, 05:14:02 pm »

Hi Subbu,

Thanks for posting this question. While I understand what you mean, I must say that 3DNA (in its current version) does not have direct means to get the job done. I may be able to come up with a solution after reading the publication associated with PDB id 2X2Q, check the PDB coordinates of the entry, and then play around with 3DNA to fit the bill. Obviously, this will take time.

To make this effort worthwhile, I'd ask you to perform a survey of other tools, e.g., UCSF Chimera, PyMol etc, to see if they already provide similar functionality. Of course, others viewers of this thread are more than welcome to jump in with their opinions. Hopefully, more users will get actively participated in such discussions that will help shape further development of 3DNA.

Xiang-Jun

1419

General discussions (Q&As) / Re: building a parallel stranded DNA

« on: September 07, 2011, 01:30:51 pm »

Hi,

Thanks for attaching the three PDB files -- they indeed clarify the issues.

Do you know the rationale of the no preserve option? It appears there can be many ways to rotate around the glycosidic bond to orient the base.

Xiang-Jun

1420

General discussions (Q&As) / Re: building a parallel stranded DNA

« on: September 07, 2011, 12:42:16 pm »

Hi Bala,

1) Firstly i tried by constructing the ps DNA from fiber model 31 but the structure i obtained was nt correct (in the sense the base pairs of chian A and C) were not in proper orientation. So i used the pdb structure as template to carry out mutation.

It seems that [red:27t8jes7]mutate_bases[/red:27t8jes7] serves your needs, right?

For the record, in fiber model #31, chains A and C form a parallel duplex with classic Hoogsteen A-U pairs. 3DNA has no problem in analyzing such structures. See the attached structure for an example:
[attachment=0:27t8jes7]fiber31_Hoogsteen.pdb[/attachment:27t8jes7]
[pre:27t8jes7]****************************************************************************
Structure classification:

This is a parallel duplex structure
****************************************************************************[/pre:27t8jes7]

2) I am not getting what example you need, in case if it is related to chimera software, you can refer this page. It is freely down loadable.

When you talk about the '[red:27t8jes7]swapna[/red:27t8jes7]' command with '[red:27t8jes7]preserve[/red:27t8jes7]' set to TRUE or FALSE, it would be helpful to be concrete by using examples. More specifically, you start with a structure in PDB format, and try to mutate a base to another one -- you have two results by setting '[red:27t8jes7]preserve[/red:27t8jes7]' to either TRUE or FALSE. If you attach these three PDB files, then things would be much clearer even for those who are not familiar with the UCSF chimera software.

Xiang-Jun

1421

General discussions (Q&As) / Re: 3DNA Cannot find help3dna.dat

« on: September 06, 2011, 09:58:47 pm »

Hi Sean,

It is likely that you've not properly set up 3DNA v2.0. Did you run [red:1nrkjhgd]x3dna_setup[/red:1nrkjhgd] as documented in the 2008 3DNA Nature Protocols paper?

More specifically, what's the output from running the following:

Code: [Select]

echo $X3DNABy default, if the [mono:1nrkjhgd]X3DNA[/mono:1nrkjhgd] environment variable is not set, the program will use [mono:1nrkjhgd]$HOME/X3DNA[/mono:1nrkjhgd]. That explains the error message:
[pre:1nrkjhgd]open_file </home/seanlaw/X3DNA/config/help3dna.dat> failed: No such file or directory[/pre:1nrkjhgd]
HTH,

Xiang-Jun

1422

General discussions (Q&As) / Re: building a parallel stranded DNA

« on: September 06, 2011, 12:02:13 pm »

Hi Subbu,

Kindly provide me the script 'mutate_base'. I would like to try it. I think adding it in 3DNA package would be a good option.

See my email. As I mentioned several times in the forum, it is users' feedbacks, like yours, that move the 3DNA project forward.

I would like to share one information on this regard, USCF chimera software has a command called 'swapna' with which we can just replace the base moiety. In addition it has a parameter called 'preserve' with which you can retain the glycosidic angle and position of the nitrogen forming the bond too after replacement.

But it is always better to use a script like yours when we have to do many mutations. In case your script doesnt have preserve option, could you please see if you can incorporate this preserve option in your script. I guess a similar name swap_base would be more suitable for your script.

Thanks for the info. Could you please provide an example of each? The new (ANSI C) program '[red:m67d7hlr]mutate_bases[/red:m67d7hlr]' preserves the base reference frame, and as a side effect, it retains "the glycosidic angle and position of the nitrogen forming the bond" as well.

Also can you merge all these threads so that others can view all related information in one shot. 1) Problems with mutations on DNA (Feb. 2011) 2) mutating DNA in DNA protein complex (Oct. 2007).

Excellent suggestion. I have long thought of consolidating the various source of information about 3DNA, but unable to get it done due to a lack of resources and time. This will change in the new future, so stay tuned.

Xiang-Jun

1423

General discussions (Q&As) / Re: building a parallel stranded DNA

« on: September 05, 2011, 10:53:45 pm »

Hi Subramanian,

Regarding your two questions on constructing models of parallel stranded (ps) DNA,

i) if it is possible to construct such a model using 3DNA and

3DNA does not have such a direct option. However, you may try fiber model 31 (or 32 for [red:3ckdzas2]Poly (U) : poly (A) : poly(U)[/red:3ckdzas2]), delete Us in chain B which form Watson-Crick base-pairs with As in chain A, then you get a parallel stranded Poly (U) : poly (A). You can then mutate bases to fit your needs (see below).

ii) there is an experimental structure of such ps duplex with completely different base composition, is there any way that i can use as am a template in 3DNA to model my structure.

The newly added utility program [red:3ckdzas2]mutate_bases[/red:3ckdzas2] should help. See thread "change one base pair in a double-strand DNA structure file". Please let me know if you want to have access to the program.

I may extend 3DNA's functionality to serve your specific purpose, if necessary; presumably such extension would turn out to be useful to other potential 3DNA users as well.

Xiang-Jun

1424

General discussions (Q&As) / Re: Analyzing ssDNA

« on: August 19, 2011, 09:08:53 pm »

Hi Orn,

Thanks for using 3DNA.

The error message means your ".inp" file does not match your ".pdb" file. Try:
[pre:3dmejz8w]find_pair -s your.pdb stdout[/pre:3dmejz8w]what do you get?

If that does not help solve your puzzle, please provide your ".inp" and ".pdb" files so I can check into the details.

HTH,

Xiang-Jun

1425

General discussions (Q&As) / Re: 3DNA setup at Linux

« on: August 19, 2011, 09:02:54 pm »

feixu@homestar:~/X3DNA/bin$ x3dna_setup
x3dna_setup: command not found

Try "[mono:4e0k1qpw][red:4e0k1qpw]./x3dna_setup[/red:4e0k1qpw][/mono:4e0k1qpw]". It appears that you do not have "[mono:4e0k1qpw]./[/mono:4e0k1qpw]" (your current directory) in your command search path.

HTH,

Xiang-Jun