Messages

1626

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

1627

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

1628

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

1629

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

1630

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

1631

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

1632

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

1633

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].

1634

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