Messages

1551

General discussions (Q&As) /

« on: April 05, 2007, 08:52:04 pm »

It is not an error, but for information only. It means that in your nucleic acid structure there is some O3' to P[i+1] linkage that's out of normal range (> 2.5 A is the cut off in 3DNA).  This message is associated with "analyze" instead of "find_pair". For example, it would happen with the "-s" option unless your nucleic acid structure is single strand and continuous (e.g., find_pair -s bdl084.pdb stdout | analyze). Please also refer to the thread on missing P atom in first residues.  

If anything is still unclear, please provide a repeatable example (structure) with a step-by-step description what you did and what you found.

HTH,

Xiang-Jun

1552

General discussions (Q&As) /

« on: March 03, 2007, 12:14:50 am »

Hi,

Welcome to the 3DNA community!

The program "fiber" is your friend to build long regular DNA models. Also check the topic on PDBML in this forum.

HTH,

Xiang-Jun

1553

General discussions (Q&As) /

« on: February 24, 2007, 11:37:56 am »

Then it is clear that you do not have permission set up correctly for $X3DNA/bin executables. I do not know your level of Linux/Unix, and/or access right to the /usr/local directory. But you can try the following:

Code: [Select]

export X3DNA=/usr/local/X3DNA
export PATH=$PATH:$X3DNA/bin
chmod a+rx /usr/local/X3DNA/bin/*
find_pair


Other than that, you need to consult your system administrator or local Linux/Unix expert for help.

Alternatively, you can always install 3DNA under your home directory.

HTH,

Xiang-Jun

1554

General discussions (Q&As) /

« on: February 22, 2007, 10:42:38 pm »

Hi,

Life should not be that hard! Setting up the 3DNA environment has rarely been an issue, indeed yours is the first case I've come cross over the past few years.

I noticed that you set X3DNA as

Code: [Select]

export X3DNA=/usr/local/X3DNA/i.e., with a trailing '/'. In the output error message, you have path

Code: [Select]

/usr/local/X3DNA//binNoticed the two '//' between X3DNA and bin? The error message means you have not put 3DNA bin directory into your command line search path yet.

Try the following in your current terminal, one line at a time, what did you get?

Code: [Select]

echo $SHELL
       # do you get '/bin/bash'? -- verifies you have 'bash' shell
ls /usr/local/X3DNA/bin/find_pair
       # this verifies that you indeed installed 3DNA under /usr/local
export X3DNA=/usr/local/X3DNA
       # without trailing '/'
echo $X3DNA
ls $X3DNA/bin/find_pair
       # If 3DNA is installed under /usr/local, this should print the full path
export PATH=$PATH:$X3DNA/bin
which find_pair

Please report back how it goes.

Xiang-Jun

1555

General discussions (Q&As) /

« on: February 19, 2007, 11:24:57 pm »

Yes, there is a way in 3DNA to calculate all backbone torsion angles of any nucleic acid structure in PDB format. It is as follows:

Code: [Select]

find_pair -s -t PDBFILE stdout | analyze

where option "-s" (or equivalently "-1") is used to treat the whole structure  as a continuous single helix,  needed for getting all backbone torsion angles.

The "-t" option also takes consideration of HETATM records for modified bases. Note that in the coming new release of 3DNA v2.0, "-t" will be set by default, thus it will no longer be needed.

Of course, this method assumes that the nucleotides in the PDB structure are in proper order in the 5'-->3' direction. This should normally be the case. If need arises, I will consider add a new functionality in "find_pair" to make the  nucleotides in order no matter whatever their original positionings in the PDB file are.

HTH,

Xiang-Jun

1556

General discussions (Q&As) /

« on: February 13, 2007, 08:25:04 pm »

Hi,

Regarding applying 3DNA to quadruplex, you might find this post in the forum relevant.

If your are only interested in calculate the backbone torsions and pucker of any nucleic acid structure, the following command will do the trick:

Code: [Select]

find_pair -s -t PDB_FILE stdout | analyze

HTH,

Xiang-Jun

1557

General discussions (Q&As) /

« on: February 13, 2007, 08:13:08 pm »

Hi,

Thanks for using 3DNA.

What happens if you do the following?

Code: [Select]

which find_pair
source ~/.bashrc
which find_pair


In other words, I suspect your setting is not in effect yet before running the source command, or starting another shell.

HTH,

Xiang-Jun

1558

General discussions (Q&As) /

« on: December 27, 2006, 10:36:43 pm »

Hi,

This is weird -- it certainly should not happen as far as 3DNA itself is concerned. I suspect that you have another program called "rebuild" in your command line search path, and it is ahead of $3DNA/bin.

To verify, try:

Code: [Select]

which rebuild from your shell prompt. What do you get?

Alternatively, try to run $3DNA/bin/rebuild instead of just "rebuild".

Have a try and please let me know how it goes.

Xiang-Jun

1559

General discussions (Q&As) /

« on: December 11, 2006, 09:51:08 pm »

Hi,

The problem you have is due to the wrong PDB format. Specifically, with the atom name, as shown below:

Code: [Select]

ATOM     11 N1   CYT     1    -278.189 335.614  -8.159                       N
instead of the correct format as in:
ATOM      9  N1    C A   1      18.770  29.711  23.733  1.00  7.31           N

In the coming new release of 3DNA, I have taken such case into consideration, and the input file following "find_pair" would be:

Code: [Select]

iBdnaVacFINAL_x3dna2.pdb
iBdnaVacFINAL_x3dna2.out
    2         # duplex
   10         # number of base-pairs
    1    1    # explicit bp numbering/hetero atoms
    1   21  0 #    1 | ....>-:...1_:[CYT]C-----G[GUA]:..22_:-<....  0.64  0.09 11.06  9.06 -3.63
    2   20  0 #    2 | ....>-:...2_:[CYT]C-----G[GUA]:..21_:-<....  0.65  0.01  9.87  9.04 -3.84
    3   19  0 #    3 | ....>-:...3_:[ADE]A-----T[THY]:..20_:-<....  0.11  0.09 13.97  9.06 -4.00
    4   18  0 #    4 | ....>-:...4_:[THY]T-----A[ADE]:..19_:-<....  0.14  0.08 11.22  9.06 -4.13
    5   17  0 #    5 | ....>-:...5_:[CYT]C-----G[GUA]:..18_:-<....  0.67  0.08  5.34  9.07 -3.89
    7   16  0 #    6 | ....>-:...7_:[CYT]C-----G[GUA]:..16_:-<....  0.70  0.26 16.15  8.99 -2.98
    8   15  0 #    7 | ....>-:...8_:[THY]T-----A[ADE]:..15_:-<....  0.29  0.29 13.17  9.06 -3.49
    9   14  0 #    8 | ....>-:...9_:[ADE]A-----T[THY]:..14_:-<....  0.21  0.01  1.70  9.21 -4.69
   10   13  0 #    9 | ....>-:..10_:[CYT]C-----G[GUA]:..13_:-<....  0.66  0.05 17.87  9.01 -3.34
   11   12  0 #   10 | ....>-:..11_:[CYT]C-----G[GUA]:..12_:-<....  0.60  0.10 12.40  9.06 -3.58
##### Base-pair criteria used:   4.00 15.00  2.50 65.00  4.50  7.50 ON
##### 0 non-Watson-Crick base-pairs, and 1 helix (0 isolated bps)
##### Helix #1 (10): 1 - 10  ***broken O3'[i] to P[i+1] linkage***


For the time being, you could write a script to change the atom name following the PDB convention.

Xiang-Jun

1560

General discussions (Q&As) /

« on: November 27, 2006, 06:48:43 pm »

Hi Pascal,

The "dv" is the vertical distance between the two base planes -- it is actually stagger in magnitude (i.e., abs(stagger)).

Or it can be thought of as the "vertical distance between base pair origins" projected onto the mean normals of the two bases (z-axis of the bp).

The "base pair origin" is actually the geometric average of the two base origins. In 3DNA, starting from the standard base reference frame (Atomic_A.pdb etc), a least-squares fitting onto corresponding experimental base gives the base reference frame (i.e., its position [origin] and orientation [x-, y- and z-axis]).

A detailed step-by-step description of the ls-fitting procedure is provide at the 3DNA homepage technical details section. Please note that over there, the standard base coordinates used is not in the standard reference frame.

In 3DNA, you can get the output of the each base reference frame by:

Code: [Select]

find_pair -s PDB_FILE stdout | analyze
Then have a look of the file "ref_frames.dat".

HTH,

Xiang-Jun

1561

General discussions (Q&As) /

« on: November 24, 2006, 02:52:11 pm »

Hi Pascal,

Nice to communicate with you here.

The standard base reference frame is described in the Olson et al. (2001) JMB report. Specifically, the origin is defined as the center of what would a perfect Watson-Crick base-pair.

As detailed in the FAQ section of the current 3DNA homepage, the default set of parameters used in 3DNA was based on a survey of the NDB structures and is very generous to account for distorted bps. As an example, how much a H-bond distance cut-off should be choosen? Intuitively, 3.2 A would be a more reasonable value than 4.0 A. However, even with such high cut-off, some users still report "find_pair" missing some bps, which turns out that the shorted possible H-bond distance would be over 5.0 A in such bps.

That's exactly the reason that 3DNA provides the "misc_3dna.par" file for users to tune it for their specific purpose. For example, by setting d_org = 1.0, dv = 0.5, z_ang = 15, one will find only Watson-Crick base-pairs.

As far as how stagger parameter is calculated, it is the projection of the vector linking the two base origins onto the mean base z-axis. A step-by-step description of the procedure can be found in the 1997 JMB SCHNAaP paper. 3DNA uses exactly the same algorithm except for a change in reference frame.

HTH,

Xiang-Jun

1562

General discussions (Q&As) /

« on: November 16, 2006, 12:18:24 am »

Hi,

Thanks for sending me the 3 coordinate files via email -- they are helpful in clarifying the issue.

You might be interested to know that in the future, you no longer need to send us email with attachments: I have set up a file upload forum at URL:
http://3dna.rutgers.edu:8080/upload/ so that users can send related information for us to debug and solve their problems. This will also allow for storage and consistent handling of user-cases.

As to your questions, firstly, you can run find_pair on it after adding the following entries to the file baselist.dat, as documented in the FAQs:

Code: [Select]

DG5     G
DG      G
DC      C
MOL     g
DC3     C
Secondly, given the irregularity of the the G-quartet structure, the normal double strand parameters obviously no longer apply. However, you can run the following to get backbone torsion angle etc parameters (of course, watch out the chi torsion related to isoG residue):

Code: [Select]

find_pair -s L1_avstr_min.pdb stdout | analyzeYou can also

Code: [Select]

find_pair -p L1_avstr_min.pdb  multi.infoThe program identifies the two G-quartets. The file multiplets.pdb contained the structures of the multiplets, which you can extract and generate publication quality images, as referred in my previous reply.

Thirdly, with the utility program blocview, run as follows:

Code: [Select]

blocview -i=L1_view.jpg L1_avstr_min.pdb
blocview -i=L1_view_z40.jpg -z=40 L1_avstr_min.pdb

You will get the following two images:


which is the default,  and
,
with a rotation about z-axis by 40 degress to make it "vertical". The color coding the Gs and Cs make them clearly distinguished, and the black minor groove edges of Gs are also obvious, and of course, the stacking ...

The 3 in 3DNA certainly not only stands for 3-dimension, but also the three integrated parts: analysis, rebuilding and visualizaion. Such block view images have been used in the NDB, and PDB. Somehow, it has not been widely adopted by the 3DNA community at large. I am just taking this opportunity to illustrate some of the not-commonly used features.

HTH,

Xiang-Jun

1563

General discussions (Q&As) / Re: Analyzing a PDB containing isolated bases

« on: November 15, 2006, 11:35:47 pm »

Dear Claudio,

Thanks for using 3DNA and your nice words about our work. Actually, as I mentioned in previously replies in this forum, it is the 3DNA users that are driving the further refinement and development of the package. Every user's question provide us a new prospective and opportunity to "Kaizen" (improve/refine) it.

Now back to your question, it is okay to run 3DNA on a nucleic acid structure without backbone atoms. The program "find_pair" will find the pairs and "analyze" will provide a detailed output of strucural parameters. Please have a look of the user's manual. The files "bp_step.par" and "bp_helical.par" are mainly for rebuilding purpose.

It will take time to get familiar with 3DNA and to use it more efficiently. If you have any further questions, please come back to this forum. In case you have some specific problems, you can attach your files and we will look into them.

HTH,

Xiang-Jun

1564

General discussions (Q&As) /

« on: November 13, 2006, 10:27:15 pm »

Hi Surjit,

Thanks for clarifying the CONECT record issue in PDBML. I am aware of the PDB HET Group Dictionary, and that is not the issue here. 3DNA generated fiber models and arbitrary strcutures mostly contains only standard residues.

The geometry that links residue i and i+1 for the "rebuild" structures may not be within standard range, thus RasMol, for examle, will generate both extraneous bonds, and missing bonds. Here is an arbitrary example just to illustrate my point:

Code: [Select]

[1] to generate the input file in tst.inp
regular_dna tst.inp

Six base-pair parameters (Dft: 0s) in the order of:
Shear  Stretch  Stagger  Buckle  Propeller  Opening
0 0 0 34 45 0

Six step parameters in the order of:
Shift  Slide  Rise  Tilt  Roll  Twist
0 0 3.4 0 25 30

Input your base sequence with only A,C,G & T:
1. From a data file (complete sequence)
2. From keyboard (enter only the repeating sequence)
Your choice (1 or 2, Dft: 2):

Repeating unit (Dft: A):
Repeating unit: A
Number of repeats (Dft: 10):

[2] to generate the PDB file with standard B-DNA backbone conformation
cp_std BDNA
rebuild -atomic tst.inp tst.pdb

[3] display in RasMol, with correct connections:
rasmol tst.pdb

[4] manually delete the CONECT records in the above tst.pdb file (tst_nocnt.pdb), and use RasMol to display it again to see what you get.


Here are the links to the three files: tst.inp, tst.pdb, tst_nocnt.pdb for you to check against/play with.

In such cases, 3DNA makes efforts to generate the correct linkages both within residue and between residues. With full CONECT info, RasMol will display properly, otherwise, its interally generated linkages may not be desirable. I am not sure how such initial distorted structure would effect MM/MD calculations, though. This is one of the examples of the details that have been taken into considerations in 3DNA.

Anyway, I have also modified "rebuild" to output PDBXML, and I am testing the code, and the new 3DNA homepage for a new release after 4 years of v1.5 ... I will keep you informed.

Best regards,

Xiang-Jun

PS. This thread is the most-visited in the 3DNA forum so far ... thanks for your involvement!

1565

General discussions (Q&As) /

« on: November 13, 2006, 09:45:13 pm »

Thanks for using 3DNA.

Please refer to  3DNA FAQs on how modified bases are handled in 3DNA, and a working example. Basically, it should be a straightforward process, and the simple scheme works for all the cases we are aware of so far. As far as base-pair parameter goes, the method should also work for the isonucleotide. However, since the base in isonucleotide is not connected to the C1' sugar  atom, the lambda virtual angle and the chi torsion angles will not be what you wanted.

As to the analysis of G-quartet structure, please have a look of the README file in the directory Examples/Triplex in 3DNA distribution. If you follow the directions there and play around a little bit, you would have a better understanding of how 3DNA can be applied in normal nucleotide structures. Again, for the isonucleotide structures, some special handling might be necessay. Could you please send me some sample isonucleitde structures (via email) so I can have a look?

Thanks,

HTH,

Xiangjun

1566

General discussions (Q&As) /

« on: November 03, 2006, 10:34:34 pm »

Dear Arvind,

Thanks for your question regarding calculating the pitch and radius of a DNA superhelix using 3DNA. Unfortunately, it is not possible to perform such calculations in the current version. I do, however, have a interest in adding such functionality in future release of 3DNA. To this end, we need users' collaboration: do you have some literature references in this regard, and could you provide me some example structures with known pitch and radius parameters? I have some general idea and need to work on some specific examples to make sure it is practical.

Thanks,

Xiang-Jun

PS. We are currently testing the new 3DNA server using this forum, and it seems pretty stable. In the near future, the 3DNA homepage will hosted here, with a new interface. We are planning to add databased driven  dynamic pages ...

1567

General discussions (Q&As) /

« on: October 23, 2006, 11:38:51 pm »

Hi Surjit,

Thanks for your help. I have added the -xml option to 'rebuild' which is used to build arbitrary nucleic acid structures based on users' input file. Do you know how to add CONECT records in PDBML? I can't find the schema for it. The program 'rebuild' also gives complete linkage info in PDB CONECT records for structures with backbone. This is to avoid erroneous connections for distorted structures in some visualization programs like RasMol.

Adding -xml option for PDBML output is a good example of how valuable users like you get involved in 3DNA's further improvements/development. It is also the reason that whenever possible, I've been trying hard to get back to users' question as quick and concrete as possible.

Best regards,

Xiang-Jun

1568

General discussions (Q&As) /

« on: October 10, 2006, 10:43:27 pm »

I am well aware of the issue you experienced here. As documented in the FAQ section of the 3DNA home page, the geometry-based algorithm implemented in "find_pair" works well for what it has been designed for. This is one of the key utility programs in 3DNA that has made it possible to analyze nucleic acid related structure automatically. BTW, it is the method used in the NDB as well.

In your case, "find_pair" does find the pair, only not the ones you would expect intuitively. As you mentioned "... looking at the structure with VMD and it does look like a mess around these residue locations." As currently implemented in "find_pair", for example, T46 is thought to better match with T101 than with A102. If you could provide me with some typical example structures (via email), I will try to see if I could improve the situation.

In your case, if the 250,000 snapshots correspond to the same structure (thus with the same bps), you could simply start with one that works and modify it for all the others (only the top two lines). Have a look at http://rutchem.rutgers.edu/~xiangjun/3DNA/manual.html for a description of the format from "find_pair". I think you do not have to run "find_pair" for each of the 250,000 snapshots.

Have a try and let me know how it goes. Please also send me some sample structures with this problem via email.

Xiang-Jun

1569

General discussions (Q&As) /

« on: October 10, 2006, 12:13:20 am »

Hi Surjit,

Hopefully you are still checking back this forum earlier than until the end of the week when I had hoped to get back to you...

Now I have the first version of -xml option ready, currently only with the "fiber" utility program. Here are two sample files: fb_atcg.xml for a fiber B-DNA model of sequence ATCG, using the default PDBML format; and fb_atcg_simplified.xml for the simplified representation of the ATOM records. Please check to see if they are valid since I do not have a software to display PDBML files. Of course, please let me know if anything you feel that can be improved. I will then add this option to "rebuild" which is the program you are currently using in your DNA MD server.

Best regards,

Xiang-Jun

1570

General discussions (Q&As) /

« on: October 09, 2006, 09:42:14 pm »

Hi,

Thanks for your feedback. I will check around to see if I can have access to SGI Altix Linux to get a compiled 3DNA version for you. We are closing for the new release of 3DNA v1.6. As noted in the FAQ, per Rutgers University policy, 3DNA is only distributed in binary form. Personally, I have access to PC Linux, Mac OS X, and Windows XP etc, which are the most common, but  certainly not complete. I will check with Dr. Olson to see if it would be feasible to allow for some users to help compile 3DNA.

Best regards,

Xiang-Jun

1571

General discussions (Q&As) /

« on: October 06, 2006, 10:45:36 pm »

Dear Surjit,

Thanks for your feedback. PDBML is certainly more general and standard, and is the way to go. I will have a look of this matter in more detail, and make changes in 3DNA accordingly. The -wide option for PDB structure output will be changed to -xml. Hopefully, I could find time to get this done by next week.

Best regards,

Xiang-Jun

1572

General discussions (Q&As) /

« on: October 05, 2006, 10:02:58 pm »

Hi,

As you guessed, h-twist stands for helical twist. More background info can be found in this email before the 2003 Albany conversation.

Basically, shift, slide, rise, tilt, roll and twist describes the bp stacking geometry, and x-displacement, y-displacement, helical rise, inclination, tip, and helical twist describes the helical geometry. For an ideal B-DNA structure, rise and helical rise would be identical, so are twist and helical twist. For A-DNA, where the bps are not perfectly parallel, you will see a clear difference between the two sets (please also refer to Figure 4 in the 3DNA paper).

In 3DNA definition, the two sets of parameters are rigorously convertible, as seen in eqs. 3 and 4 of 3DNA paper. There is a utility program named 'step_hel' which converts between the two sets of parameters for your verification.

In general use, people talk more about slide/roll/twist etc than x-disp, helical rise etc.

HTH,

Xiang-Jun

1573

General discussions (Q&As) /

« on: October 04, 2006, 11:04:57 pm »

Hi Surjit,

Thanks for using 3DNA in your MD web server.

I am aware of the PDB f8.3 coordinate limitation. In the current version of 3DNA the xyz coordinates are reset if they are possibly out of range. However, as you see, the problem can't be solved within PDB format.

In the coming new release of 3DNA v1.6, I've added a new command line option -w for wide output in pseudo-PDB file, as follows:

Code: [Select]

"%6s%8ld %4s %3s %c %6ld %15.5f%15.5f%15.5f
This is a simplified solution which requires little parsing work for those who  need large structures. Of course, I will also consider a more standard, general approach, e.g., adopting PDBML as an output option, if feasible. Could you please provide me with more details on it? What's the minimum that needs to be done to convert the PDB to PDBML? Let's work this out before the new 3DNA release.

3DNA is only available in binary form, per Rutgers University policy.

Best regards,

Xiang-Jun

1574

General discussions (Q&As) /

« on: October 03, 2006, 08:56:00 pm »

Hi,

Thanks for your interest in using 3DNA. The issue you have seems to relate more to hardware architecture of SGI than to the Intel-based PC Linux. The Redhat binary of 3DNA runs Okay on all the Intel-based PC Linux system in my experience, including SUSE 9 which I have access to and have just verified.

A similar problem happens to the 3DNA Mac OS X binary which does not runs on the new Intel-based Mac OS X system.

What happens if you download the SGI version?

The current download of 3DNA is v1.5, released at the end of 2002, which is quite stable and robust. Over the years, however, there have been numerous improvements including minor bug fixes and newly added functionality etc. We are close to a new release v1.6 in the new future, and we will try to cover the mostly commonly used OSes.

BTW, how common is SGI running Linux?

Xiang-Jun

1575

General discussions (Q&As) /

« on: September 29, 2006, 10:45:13 pm »

Hi Fei,

If I understand you correctly, you are looking for the middle-reference-frame, which is available from file auxiliary.par after  running analyze on a duplex struture. An example would be as follows:

Code: [Select]

find_pair bdl084.pdb stdout | analyzeCheck file auxiliary.par, the section you are looking for is:

Code: [Select]

*****************************************************************************************
Local middle reference frames
                Ox      Oy      Oz     Xx    Xy    Xz   Yx    Yy    Yz    Zx    Zy    Zz
   1 CG/CG    16.84   25.38   24.41 -0.90  0.43 -0.02  0.40  0.82 -0.41 -0.16 -0.38 -0.91
   2 GC/GC    16.36   24.39   21.11 -0.46  0.84 -0.28  0.86  0.36 -0.36 -0.20 -0.40 -0.89
   3 CG/CG    16.17   23.28   17.92  0.11  0.90 -0.41  0.98 -0.17 -0.12 -0.18 -0.39 -0.90
   4 GA/TC    15.72   21.96   15.03  0.62  0.71 -0.33  0.77 -0.63  0.07 -0.16 -0.30 -0.94
   5 AA/TT    15.07   21.01   11.89  0.96  0.19 -0.20  0.24 -0.94  0.26 -0.14 -0.30 -0.94
   6 AT/AT    14.73   20.48    8.65  0.92 -0.39 -0.03 -0.36 -0.87  0.33 -0.16 -0.29 -0.94
   7 TT/AA    14.44   19.97    5.45  0.57 -0.81  0.13 -0.80 -0.52  0.30 -0.17 -0.27 -0.95
   8 TC/GA    14.15   19.36    2.16 -0.05 -0.97  0.25 -0.99  0.09  0.14 -0.16 -0.24 -0.96
   9 CG/CG    13.18   18.67   -0.90 -0.59 -0.74  0.31 -0.78  0.62  0.01 -0.20 -0.24 -0.95
  10 GC/GC    12.62   18.30   -4.04 -0.93 -0.27  0.23 -0.31  0.94 -0.14 -0.18 -0.20 -0.96
  11 CG/CG    12.80   18.15   -7.43 -0.93  0.35  0.11  0.33  0.93 -0.18 -0.16 -0.13 -0.98
*****************************************************************************************

HTH,

Xiangjun