Messages

1551

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

1552

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!

1553

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

1554

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 ...

1555

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

1556

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

1557

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

1558

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

1559

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

1560

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

1561

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

1562

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

1563

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

1564

General discussions (Q&As) /

« on: August 24, 2006, 09:01:05 pm »

The problem you have is because of the non-standard atomic names of the modified 8oxoguanine.  This will become immediately obvious if you display this residue using Rasmol and "label %a". For example, you do not have the " N9 " atom, instead you have " N4 " connecting to " C6 ". 3DNA uses the standard atomic names to identify a residue.

Code: [Select]

ATOM      1  O1  8og     1       3.537   1.423  -0.000  1.00  0.00
ATOM      2  C4  8og     1       3.852   0.232  -0.000  1.00  0.00
ATOM      3  N1  8og     1       2.854  -0.789  -0.000  1.00  0.00
ATOM      4  C1  8og     1       3.077  -2.143  -0.000  1.00  0.00
ATOM      5  N5  8og     1       1.984  -2.956  -0.000  1.00  0.00
ATOM      6  N2  8og     1       4.278  -2.684  -0.000  1.00  0.00
ATOM      7  C2  8og     1       5.269  -1.754  -0.000  1.00  0.00
ATOM      8  C3  8og     1       5.134  -0.380  -0.000  1.00  0.00
ATOM      9  N3  8og     1       6.409   0.160  -0.000  1.00  0.00
ATOM     10  C5  8og     1       7.365  -0.843  -0.000  1.00  0.00
ATOM     11  O2  8og     1       8.589  -0.742  -0.000  1.00  0.00
ATOM     12  N4  8og     1       6.615  -2.035  -0.000  1.00  0.00
ATOM     13  C6  8og     1       7.224  -3.350  -0.000  1.00  0.00In addition, there is already an entry for 8OG in file baselist.dat

Code: [Select]

8OG     g      #       pdb1fyi
so you need not to add an extra line for it. Indeed it helps to download pdb1fyi to see how atoms are named for 8OG over there.

When adding a new base into baselist.dat, please use all uppercase letters: thus use "8OG" instead of "8og".

HTH,

Xiang-Jun

1565

General discussions (Q&As) / Re: DNA standards/statistics using 3DNA

« on: August 18, 2006, 10:38:37 pm »

Dear Les,

Thanks for your kind words regarding 3DNA. It's been my pleasure to see it so widely accepted by the community. Over the years, I have taken each user's question as an opportunity to improve it.

Now back to your question. I have dug out the TA-DNA structures used in our 3DNA paper, and they are as follows:

Code: [Select]

pd0070, pd0112, pd0154, pd0155, pd0156 pd0157, pd0158, pd0159, pd0160,
pd0161, pd0162, pd0163, pd0164, pdr031 pdt009, pdt012, pdt024, pdt025,
pdt032, pdt034, pdt036

This directory contains TATA box segments. It is normally 8-bp long, and
has the sequence: T-A-T-A-@-A-@-N. There are two kinks at the terminal
steps.

* means non-WC base-pair which is eliminated from further analysis

NDB ID  ##     Sequence      Res(A)  R-fac(%) chainID and residue range
--------------------------------------------------------------------
pd0070  01  T-T-T-A-A-A-T-A   2.4     20.0   C 1410 1417 D 1432 1439
                           
pd0112  02  T-A-T-A-A-A-A-G   2.65    23.1   K 8 15 L 105 112
        03  T-A-T-A-A-A-A-G                  C 8 15 D 105 112
        04  T-A-T-A-A-A-A-G                  G 8 15 H 105 112
        05  T-A-T-A-A-A-A-G                  O 8 15 P 105 112
        06  T-A-T-A-A-A-A-G                  S 8 15 T 105 112
                                     
pd0154  07  T-A-T-A-A-A-A-T   1.86    21.0   C 203 210 D 219 226
        08  T-A-T-A-A-A-A-T                  E 203 210 F 219 226
                                   
pd0155  09  T-A-T-A-A-G-A-G*  1.93    19.6   C 203 209 D 220 226
        10  T-A-T-A-A-G-A-G*                 E 203 209 F 220 226
   
pd0156  11  T-A-T-A-A-T-A-G*  2.1     19.3   C 203 209 D 220 226
        12  T-A-T-A-A-T-A-G*                 E 203 209 F 220 226
                                   
pd0157  13  T-A-T-A-T-A-A-G*  2.3     19.4   C 203 209 D 220 226
        14  T-A-T-A-T-A-A-G*                 E 203 209 F 220 226
                                   
pd0158  15  T-A-T-T-A-A-A-G*  2.1     19.4   C 203 209 D 220 226
        16  T-A-T-T-A-A-A-G*                 E 203 209 F 220 226
                                   
pd0159  17  T-A-C-A-A-A-A-G*  1.9     20.9   C 203 209 D 220 226
        18  T-A-C-A-A-A-A-G*                 E 203 209 F 220 226
   
pd0160  19  T-T-T-A-A-A-A-G*  1.8     19.3   C 203 209 D 220 226
        20  T-T-T-A-A-A-A-G*                 E 203 209 F 220 226
                                     
pd0161  21  T-A-T-A-A-A-T-G*  2.23    19.1   C 203 209 D 220 226
        22  T-A-T-A-A-A-T-G*                 E 203 209 F 220 226
                                     
pd0162  23  A-A-T-A-A-A-A-G*  2.3     18.2   C 203 209 D 220 226
        24  A-A-T-A-A-A-A-G*                 E 203 209 F 220 226
                                     
pd0163  25  T-A-T-A-A-A-A-G   1.9     19.7   C 203 210 D 219 226
        26  T-A-T-A-A-A-A-G                  E 203 210 F 219 226
                                     
pd0164  27  T-A-T-A-A-A-C*G*  1.95    19.9   C 203 208 D 221 226
        28  T-A-T-A-A-A-C*G*                 E 203 208 F 221 226
                                     
pdr031  29  T-T-T-t-t-A-A-A   2.1     21.2   C 1408 1415 E 1420 1427
                                     
pdt009  30  T-A-T-A-A-A-A-G   2.25    20.2   A 203 210 B 305 312
        31  T-A-T-A-A-A-A-G                  C 403 410 D 505 512
                                     
pdt012  32  T-A-T-A-T-A-A-A   1.8     20.1   C 2 9 C 21 28
        33  T-A-T-A-T-A-A-A                  D 2 9 D 21 28
                                     
pdt024  34  T-A-T-A-T-A-T-A   2.9     21.4   B 103 110 C 115 122
                                     
pdt025  35  T-A-T-A-A-A-A-G   1.9     19.4   C 203 210 D 219 226
        36  T-A-T-A-A-A-A-G                  E 303 310 F 319 326
                                     
pdt032  37  T-A-T-A-A-A-A-G   2.7     21.5   C 4 11 D 106 113
                                     
pdt034  38  T-A-T-A-A-A-A-G   1.9     18.9   B 5 12 C 105 112
                                     
pdt036  39  T-A-T-A-A-A-A-C   2.5     23.5   E 9 16 F 1 8


When time permits, I will put the A-DNA and B-DNA structures used in 3DNA paper on 3DNA wiki as well.

HTH,

Xiang-Jun

PS. See the thread "Datasets and scripts for reproducing Figure 5 of the 3DNA NAR03 paper" for final details [added 2012-09-07].

1566

General discussions (Q&As) / Re: Missing P atom in first residues- error

« on: August 17, 2006, 09:53:49 pm »

Dear NARENDRA,

Thanks for being the first 3DNA user to try out this forum!

No, these are not error messages -- they are there for information only, noting the fact that some atoms are missing from a base residue. In this case, you will find that some backbone torsion angles involving these atoms will be missing from the main output file.

For example, with bdl084, the output will be:

Code: [Select]

Strand I
  base    alpha    beta   gamma   delta  epsilon   zeta    chi
   1 C     ---     ---    -70.0   144.7  -171.8   -98.4  -105.9
   2 G    -69.8  -172.2    43.0   148.1  -151.3  -157.0   -85.4
   3 C    -39.4   130.5    50.1    93.3  -165.4   -81.2  -132.4


HTH,

Xiang-Jun

When I run X3DNA I get the following error. I do not have a phosphate group on the first residue, so can this error be ignored?

Residue 3 and 21 are first residues in each strand.

 ...... reading file: baselist.dat ......
missing " P  " atom : residue name   A, chain  , number    3
missing " P  " atom : residue name   A, chain  , number   21