Messages

1

Feature requests / Mutate_Bases: Option to mutate all residues of the same type to another

« on: April 20, 2012, 10:24:15 am »

Xiang-Jun,

I am playing with mutating 1RNA.pdb (contains only A/U) into a structure that contains only C/G (G for A and C for U).  This is not vital but it would be nice if there was an option to convert ALL of the A's to G's (or whatever is needed) and all of the U's to C's.  The current functionality is perfectly fine for a few point mutations but this added capability would be helpful and make the process less tedious having to create a file to list out all of the individual mutations.  I can also see a logical negation to be useful as well.  For example, mutate all of the A's to G's except for residue 5 and residue 7.

Again, the program works great so this would only be a wish-list request.

Thank you for your time, effort, and continued support of 3DNA!

2

RNA structures (DSSR) / Re: Single-Stranded Based Zp Parameter

« on: April 19, 2012, 06:05:44 pm »

Xiang-Jun,

Thanks for your explanation(s).  Everything looks okay from here based on the tests that I've done.  I've also successfully added this option to my 3dna.pl Perl script.  I'm going to begin analyzing some simulations and hopefully be able to find more things to say.

3

RNA structures (DSSR) / Re: Single-Stranded Based Zp Parameter

« on: April 19, 2012, 05:04:18 pm »

To be clear, the PDB file that I am using only contains RNA residues 175-177 and no other atoms or residues.

4

RNA structures (DSSR) / Re: Single-Stranded Based Zp Parameter

« on: April 19, 2012, 05:00:26 pm »

Xiang-Jun,

Thanks for the quick reply.  The 1JJ2 test case works and I can now see the proper output.  I tried to add this to my 3dna.pl Perl script but quickly found out that a command like the following doesn't work:

find_pair PDB.file OUT.file
analyze -t=test.tor -c OUT.file

The test.tor file doesn't write (and possibly doesn't calculate) anything aside from some title information.  I'm guessing that the "-t" and "-c" options cannot be used together.

However, this works

analyze -t=test.tor PDB.file

5

RNA structures (DSSR) / Single-Stranded Based Zp Parameter

« on: April 19, 2012, 02:55:55 pm »

Xiang-Jun,

I read your recent post about this parameter and was intrigued by Richardson's observation.  Thus, I download v2.1 today (32-bit Ubuntu version) in order to calculate this new Zp parameter.  However, when I run 3DNA on the test case that you discussed (1JJ2.pdb) I can't seem to find where the new parameter is listed.  I see the old dinucleotide Zp parameter but they obviously don't correspond to the values that you had shown (1.9 Angstroms and 4.4 Angstroms).  Perhaps binaries have not been updated yet?

Also, if I'm only interested in the single-stranded based Zp value then can I safely assume that I can simply extract the G175 and U176 residues out from the large PDB structure and still be able to calculate the Zp values.  In other words, since it doesn't rely on base pair information then I don't need the rest of the structure.  Is that correct? 

Finally, since your new single-stranded based Zp parameter does not produce values that exactly match those from the Richardson definition (for the 1JJ2 structure: 2.2 Angstroms and 4.6 Angstroms using the Richardson definition vs. your definition - see above), does that mean that I would need to use a slightly different cutoff value instead of 2.9 Angstroms?  From the 1JJ2 example, perhaps using a value of 3.15 Angstroms is better for 3DNA (1.9 A - 2.2 A = -0.3 A, 4.4 A - 4.6 A = -0.2 A)?

Thank you for your time.

6

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

« on: September 06, 2011, 05:44:28 pm »

Hi,

I downloaded 3DNA v2.0 and have installed it on a Linux machine.  However, upon executing find_pair I get the error:

open_file </home/seanlaw/X3DNA/config/help3dna.dat> failed: No such file or directory


Of course, find_pair is installed in:

/home/seanlaw/Programs/X3DNA/bin

I'm not sure why find_pair is trying to look in that particular directory and what I can/need to do to have find_pair look in

/home/seanlaw/Programs/X3DNA/config

instead...

Any help or suggestions would be greatly appreciated.  Thanks

Sean

P.S.  I tried searching for help3dna.dat but found nothing.

7

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

« on: February 10, 2011, 06:27:05 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.

Using the MMTSB Toolset:

processDCD.pl -apply "3dna.pl -groove major" template.pdb dna.dcd > output

The typical 3DNA output will print to the screen while the major groove information will be written to the output file and should look like:

1 0.0750 major --- --- --- 17.2 17.4 16.4 17.4 18.7 --- --- ---
2 0.1500 major --- --- --- 17.1 17.3 16.4 17.4 18.9 --- --- ---
3 0.2250 major --- --- --- 17.2 17.6 16.2 17.4 19.1 --- --- ---
4 0.3000 major --- --- --- 17.4 17.5 15.9 17.3 19.1 --- --- ---
5 0.3750 major --- --- --- 17.8 17.7 15.6 17.1 19.0 --- --- ---
6 0.4500 major --- --- --- 18.0 18.0 15.4 17.2 19.0 --- --- ---
7 0.5250 major --- --- --- 18.1 18.1 15.3 17.2 19.1 --- --- ---
8 0.6000 major --- --- --- 18.0 18.3 15.4 17.3 19.2 --- --- ---
9 0.6750 major --- --- --- 18.1 18.8 15.4 17.4 19.3 --- --- ---
10 0.7500 major --- --- --- 18.2 19.0 15.3 17.5 19.4 --- --- ---
11 0.8250 major --- --- --- 18.2 19.3 15.4 17.4 19.4 --- --- ---
12 0.9000 major --- --- --- 18.1 19.1 15.6 17.3 19.3 --- --- ---
13 0.9750 major --- --- --- 18.2 19.0 15.5 17.2 19.3 --- --- ---
14 1.0500 major --- --- --- 18.3 18.6 15.2 17.4 19.1 --- --- ---
15 1.1250 major --- --- --- 18.4 18.4 15.1 17.6 19.1 --- --- ---
16 1.2000 major --- --- --- 18.5 18.2 15.3 17.6 19.2 --- --- ---
17 1.2750 major --- --- --- 18.6 18.2 15.3 17.7 19.3 --- --- ---
18 1.3500 major --- --- --- 18.8 18.0 15.1 17.8 19.5 --- --- ---
19 1.4250 major --- --- --- 18.7 18.1 15.1 17.8 19.8 --- --- ---
20 1.5000 major --- --- --- 18.7 18.0 15.1 17.8 19.7 --- --- ---


The first column is just the row number, the second column is the simulation time and the remaining columns is output as per 3dna.pl (see above).

Hope this helps.

Seam

8

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

« on: February 04, 2011, 09:29:05 pm »

Xiang-jun,

Thank you for your kind words.  A little side note, the MMTSB Tool Set is developed (in collaboration with other labs) by members of my lab (Feig Lab @ Michigan State University) and hence, I am an active user of this useful toolset.  The 3dna.pl script was written by me to (hopefully) accurately decipher the verbose 3DNA output.  I make a special effort to document most/all of my code because it is helpful and also because I am forgetful.  I too hope that this script will aid others in their applications using 3DNA.

Sean

9

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

« on: February 03, 2011, 05:36:49 pm »

In order to use this with the MMTSB Tool Set and to process a CHARMM/NAMD trajectory file, use "processDCD.pl"

processDCD.pl -apply "3dna.pl -groove major" template.pdb trajectory.dcd

This will apply the command "3dna.pl -groove major" to each simulation frame of trajectory.dcd.  It is important that the template.pdb matches the trajectory.dcd!

10

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

« on: February 03, 2011, 05:34:03 pm »

Hi All,

Please see the attached Perl script that can be used in conjunction with 3DNA (assuming that it is already installed).

# 3dna.pl -h

Usage:   3dna.pl [-options] <PDBfile>
Options: [-show all|none|out|inp|key1:keyn]
         [-inp name]
         [-setinp name]
         [-type]
         [-ref name [offset]]
         [-madbend]
         [-axis]
         [-groove minor|major|all]
         [-par shear|stretch|stagger|buckle|propel|open|all]
         [-step shift|slide|rise|tilt|roll|twist|all]
         [-helix x|y|hrise|incl|tip|htwist|all]
         [-pucker ampl|phase|both|pucker|all]
         [-torsion alpha|beta|gamma|delta|epsilon|zeta|chi|all]

To use this script, simply provide a valid PDB file.  For example:

$ 3dna.pl -groove major 1bna.pdb

major --- --- --- 17.3 17.3 16.3 17.4 18.4 --- --- ---

The hyphens correspond to parts of the structure where measurements could not be performed.  The order of the output is according to the base pairs from 3DNA and can be extracted by using the "-ref name" option.  Using "-ref" will produce a reference file that tells you what the base pair order is:

$ 3dna.pl -groove major -ref ref.out 1bna.pdb

Looking at the reference file we see:

major(1) BP1:1-24(2) BP2:2-23(3) BP3:3-22(4) BP4:4-21(5) BP5:5-20(6) BP6:6-19(7) BP7:7-18( BP8:8-17(9) BP9:9-16(10) BP10:10-15(11) BP11:11-14(12)

The brackets corresponds to the column from the major groove output.  Thus, the first column tells you that the original output is for the major groove, the second column is base pair 1 (BP1) which is formed between base 1 and base 4, the third column is base pair 2 (BP2) which is formed between base 2 and base 23, and so on.  

$ 3dna.pl -groove all -ref ref.out 1bna.pdb

This gives you both the major and minor grooves:

minor major --- --- --- --- --- --- 12.0 17.3 10.5 17.3 9.9 16.3 9.3 17.4 9.9 18.4 --- --- --- --- --- ---

However, now both grooves are listed with the reference file looking like:

minor(1) major(2) BP1:1-24(3) BP1:1-24(4) BP2:2-23(5) BP2:2-23(6) BP3:3-22(7) BP3:3-22( BP4:4-21(9) BP4:4-21(10) BP5:5-20(11) BP5:5-20(12) BP6:6-19(13) BP6:6-19(14) BP7:7-18(15) BP7:7-18(16) BP8:8-17(17) BP8:8-17(18) BP9:9-16(19) BP9:9-16(20) BP10:10-15(21) BP10:10-15(22) BP11:11-14(23) BP11:11-14(24)

The other measurements are done the same way and multiple measurements can be combined and parsed at the same time:

$ 3dna.pl -groove major -torsion alpha 1bna.pdb

major --- --- --- 17.3 17.3 16.3 17.4 18.4 --- --- --- alpha --- -65.6 -62.6 -62.9 -43.0 -73.3 -56.6 -59.2 -58.5 -67.3 -73.9 -81.5 -65.0 -72.2 -66.8 -59.1 -58.6 -58.3 -57.1 -56.6 -69.2 -63.0 -51.3 ---

Here the major grooves are displayed first followed by the alpha values in order.

More documentation can be found in the header section as comments in the script itself.  Please feel free to e-mail me at slaw@msu.edu if you have any questions, comments, or concerns.

Sean

11

MD simulations / MMTSB Tool Set for CHARMM/NAMD generated trajectory DCD files

« on: January 31, 2011, 01:34:32 pm »

Xiang-Jun,

I just wanted to add that for simulations generated from CHARMM/NAMD that produce trajectory files in a binary format (sometimes named "DCD" files), one could use the MMTSB Tool Set:

http://blue11.bch.msu.edu/mmtsb/Main_Page

Click "Download" in the menu.

Although the MMTSB Tool Set was created in an effort to make simulating in CHARMM much easier, there is a script called "processDCD.pl" that, if used in the right way, can be used in conjunction with 3DNA (I've done this myself):

http://blue11.bch.msu.edu/mmtsb/processDCD.pl

I would be happy to share my experiences with using the MMTSB Tool Set.

Sean

12

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

« on: December 09, 2010, 12:59:05 pm »

Hi all,

Yes, the blog explained exactly what I needed to do.

1) Generate an input file using find_pair
2) Use this input file in the analyze program for all frames

Thanks again!

13

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

« on: December 08, 2010, 05:18:22 pm »

Hi,

I found this blog post by Xiang-Jun that discusses exactly this topic:

http://xiang-jun.blogspot.com/2010_07_18_archive.html

I will report back with my experience.

14

General discussions (Q&As) / Missing Groove Measurement

« on: December 08, 2010, 05:09:51 pm »

Hi All,

I am calculating the major and minor groove distances using 3DNA from different snapshots from an MD simulation.  I noticed that in one snapshot 3DNA reports the major/minor groove measurements for 16 base pairs and in a later snapshot 3DNA only reports major/minor groove values for 15 base pairs.  I should point out that there are significant dynamics in my DNA molecule that is correlated with the missing base pair but, according to the documentation, major/minor groove distances are measured based upon the P-P distance and does not depend on the helical axis.  Is there a way to force the program to calculate all such values regardless of the dynamics of the DNA?  Or is it possible to tell 3DNA exactly which bases are paired and to use the same information for all snapshots from the simulation.

Thanks,

Sean

15

General discussions (Q&As) / Re: Global Helical Axis Information Missing

« on: September 23, 2010, 11:47:08 pm »

Hi,

Thank you for your reply.  I am only interested in generating a rough helical axis so high accuracy is not important so I tried changing the parameter from 0.6 to 2.0 but I am still unable to obtain the values for the helical axis.  Does this mean that I should also change other parameters?

Sean

16

General discussions (Q&As) / Global Helical Axis Information Missing

« on: September 23, 2010, 08:16:05 pm »

Hi All,

I am trying to find the vector that describes the global helical axis for 1E3M.pdb the 1E3M.out file does not give this information.  I have tried using 3DNA on the classical 1BNA structure and I am able to obtain the global helical axis.  Any assistance for obtaining the global helical axis for 1E3M.pdb would be greatly appreciated (and an explanation for not being able to get this value is also appreciated).

Thanks in advance!

Sean

17

General discussions (Q&As) / Re: DNA Step Values for DNA Mismatches

« on: January 21, 2010, 11:25:19 am »

On a side note, I stumbled across your blog page and, per your suggestion, I tested out Valgrind on a simple piece of code which had been giving me some problems previously (and was unresolved).  Thanks to your suggestion, I was able to pinpoint and correctly identify the (memory-related) bug in my code!

Sean

18

General discussions (Q&As) / Re: DNA Step Values for DNA Mismatches

« on: January 21, 2010, 11:18:51 am »

Xiang-Jun,

Sorry that it has taken me so long to reply but I wanted to cover all of my bases before I made too many wild claims of what did/didn't work.  I should first start off by saying that I was using the older version of 3DNA (v1.5 I think) so I suspected that there would possible differences in the calculations.  Thus, I installed v2.0 but found the same problem (with respect to missing the first G-C base pair, see below).

1) I know how hard it is to remain polite and professional when posting/monitoring forums/discussions especially when people want a quick answer so I always try my best to do my homework thoroughly before asking too many dumb questions.  I think I dug into the bp_step.par file because I was trying to understand where certain values were coming from and why they existed in multiple places.  Details, as you mentioned, are important and I definitely don't want to waste any body's valuable time.  You've written a great tool in 3DNA and the support forum is a wealth of knowledge!

2) Running find_pair directly, I will try to keep that in mind next time!  

3) Originally, I had attributed the missing G-C base pair to it being the first step and glazed over that fact.  After you brought it up, I went back to look at the difference between v1.5 and v2.0.  When I run find_pair v1.5, I get the following screen output:

Command: find_pair 2O8B.pdb 2O8B.out

 ...... /home/slaw/Desktop/Programs/X3DNAv1.5/X3DNA/BASEPARS/ ......
 ...... reading file: misc_3dna.par ......

 ...... /home/slaw/Desktop/Programs/X3DNAv1.5/X3DNA/BASEPARS/ ......
 ...... reading file: baselist.dat ......
unknown residue  DG    1  on chain E [#1]
Check the base and add one more item in file <baselist.dat>

Notice that it complains about the DG residue.  As well, it is unable to produce the corresponding 2O8B.out file.  I think that this is due to the unrecognized naming convention "DG" which should be written as "GUA" instead.  This is why I had extracted the coordinates before and renamed them all to GUA, ADE, THY, and CYT.  This time, to see that 2) above works, I simply made a copy of 2O8B.pdb and changed all of the DNA nucleotides while keeping all of the other parts of the structural file intact.  Running this through find_pair produced:

...... /home/slaw/Desktop/Programs/X3DNAv1.5/X3DNA/BASEPARS/ ......
 ...... reading file: misc_3dna.par ......

 ...... /home/slaw/Desktop/Programs/X3DNAv1.5/X3DNA/BASEPARS/ ......
 ...... reading file: baselist.dat ......

 ...... /home/slaw/Desktop/Programs/X3DNAv1.5/X3DNA/BASEPARS/ ......

 ...... /home/slaw/Desktop/Programs/X3DNAv1.5/X3DNA/BASEPARS/ ......
 ...... reading file: misc_3dna.par ......

Time used: 0.17 seconds


In the v2.0 case, the output looks like:

handling file <2O8B.pdb>

 ...... /home/slaw/Desktop/Programs/X3DNA/X3DNA/config/ ......
 ...... reading file: misc_3dna.par ......

 ...... /home/slaw/Desktop/Programs/X3DNA/X3DNA/config/ ......
 ...... reading file: baselist.dat ......
uncommon residue ADP  936  on chain A [#1793] assigned to: a
uncommon residue ADP  202  on chain B [#1795] assigned to: a

 ...... /home/slaw/Desktop/Programs/X3DNA/X3DNA/config/ ......
 ...... reading file: atomlist.dat ......

 ...... /home/slaw/Desktop/Programs/X3DNA/X3DNA/config/ ......

 ...... /home/slaw/Desktop/Programs/X3DNA/X3DNA/config/ ......
 ...... reading file: atomlist.dat ......

Time used: 00:00:00:01

Instead of complaining about the DG (which I assume is "fixed" in v2.0), it complains about the ADP nucleotides which are present in the PDB file (of 2O8B.pdb, not the modified one).  Now, when I compare the ".out" file from both v1.5 and v2.0:

from v1.5:

2O8B.new.pdb
2O8B.new.out
    2         # duplex
   14         # number of base-pairs
    1    0    # explicit bp numbering/hetero atoms
    2   29  0 #    1 | E:...2_:[ADE]A-----T[THY]:..29_:F  0.89  0.82 26.82  9.09  1.03
    3   28  0 #    2 | E:...3_:[ADE]A-----T[THY]:..28_:F  0.23  0.03 18.38  9.24 -1.20
    4   27  0 #    3 | E:...4_:[CYT]C-----G[GUA]:..27_:F  0.78  0.19  8.59  8.93 -0.33
    5   26  0 #    4 | E:...5_:[CYT]C-----G[GUA]:..26_:F  0.56  0.29 17.33  9.24 -0.36
    6   25  0 #    5 | E:...6_:[GUA]G-----C[CYT]:..25_:F  0.29  0.27 19.28  9.01 -0.67
    7   24  9 #    6 x E:...7_:[CYT]C-----G[GUA]:..24_:F  0.22  0.01 24.18  9.04 -1.26
    8   23  0 #    7 | E:...8_:[GUA]G-*---T[THY]:..23_:F  5.22  0.31 43.28  9.87  5.84
    9   22  0 #    8 | E:...9_:[CYT]C-----G[GUA]:..22_:F  0.44  0.33 20.98  8.84 -0.40
   10   21  0 #    9 | E:..10_:[GUA]G-----C[CYT]:..21_:F  0.41  0.39 10.80  9.05 -0.32
   11   20  0 #   10 | E:..11_:[CYT]C-----G[GUA]:..20_:F  0.26  0.01 12.86  9.06 -1.21
   12   19  0 #   11 | E:..12_:[THY]T-----A[ADE]:..19_:F  0.85  0.47 11.88  8.95  0.28
   13   18  0 #   12 | E:..13_:[ADE]A-----T[THY]:..18_:F  0.53  0.18  9.30  8.85 -0.61
   14   17  0 #   13 | E:..14_:[GUA]G-----C[CYT]:..17_:F  1.17  0.94 21.28  8.97  1.54
   15   16  0 #   14 | E:..15_:[GUA]G-----C[CYT]:..16_:F  1.17  0.05 37.85  8.66 -0.22
##### Base-pair criteria used:   4.00 15.00  2.50 65.00  4.50  7.50
##### 1 non-Watson-Crick base-pair, and 2 helices (0 isolated bps)
##### Helix #1 (6): 1 - 6
##### Helix #2 (: 7 - 14

from v2.0:

2O8B.pdb
2O8B.out
    2         # duplex
   14         # number of base-pairs
    1    1    # explicit bp numbering/hetero atoms
    2   29  0 #    1 | ....>E:...2_:[.DA]A-----T[.DT]:..29_:F<....  0.89  0.82 26.82  9.09 -1.13
    3   28  0 #    2 | ....>E:...3_:[.DA]A-----T[.DT]:..28_:F<....  0.23  0.03 18.38  9.24 -3.78
    4   27  0 #    3 | ....>E:...4_:[.DC]C-----G[.DG]:..27_:F<....  0.78  0.19  8.59  8.93 -3.40
    5   26  0 #    4 | ....>E:...5_:[.DC]C-----G[.DG]:..26_:F<....  0.56  0.29 17.33  9.24 -3.00
    6   25  0 #    5 | ....>E:...6_:[.DG]G-----C[.DC]:..25_:F<....  0.29  0.27 19.28  9.01 -3.20
    7   24  9 #    6 x ....>E:...7_:[.DC]C-----G[.DG]:..24_:F<....  0.22  0.01 24.18  9.04 -3.55
    8   23  0 #    7 | ....>E:...8_:[.DG]G-*---T[.DT]:..23_:F<....  5.22  0.31 43.28  9.87  7.00
    9   22  0 #    8 | ....>E:...9_:[.DC]C-----G[.DG]:..22_:F<....  0.44  0.33 20.98  8.84 -2.85
   10   21  0 #    9 | ....>E:..10_:[.DG]G-----C[.DC]:..21_:F<....  0.41  0.39 10.80  9.05 -3.28
   11   20  0 #   10 | ....>E:..11_:[.DC]C-----G[.DG]:..20_:F<....  0.26  0.01 12.86  9.06 -4.07
   12   19  0 #   11 | ....>E:..12_:[.DT]T-----A[.DA]:..19_:F<....  0.85  0.47 11.88  8.95 -2.62
   13   18  0 #   12 | ....>E:..13_:[.DA]A-----T[.DT]:..18_:F<....  0.53  0.18  9.30  8.85 -3.65
   14   17  0 #   13 | ....>E:..14_:[.DG]G-----C[.DC]:..17_:F<....  1.17  0.94 21.28  8.97 -0.89
   15   16  0 #   14 | ....>E:..15_:[.DG]G-----C[.DC]:..16_:F<....  1.17  0.05 37.85  8.66 -1.83
##### Base-pair criteria used:   4.00   0.00  15.00   2.50  65.00   4.50   7.50 [ O N]
##### 1 non-Watson-Crick base-pair, and 2 helices (0 isolated bps)
##### Helix #1 (6): 1 - 6
##### Helix #2 (: 7 - 14

I notice some key differences/similarities:

i) They both contain the same number of lines.

ii) They both still do NOT contain the first G-C base pair information (even with v2.0 using an unmodified PDB file downloaded from PDB.org).

iii) The output format for v2.0 is slightly different from v1.5 (so my parsing script written in Perl will need to be modified)

iv) The final column in each row for each base step is different (-1.13 vs. 1.03).  I think I read somewhere that this value is simply being calculated differently?

v) The base-pair criteria used appears slightly different.

From this, I still can't explain why the G-C base pair is missing.

4) I will try modifying the helix break parameter as you had suggested (just for experience) but from what you said, it looks like I could just extract the pertinent information directly from the "bp_step.par" file without having to do that since it will always include a complete set of parameters.  Is that correct?

Thank you for your time.

Sean

19

General discussions (Q&As) / DNA Step Values for DNA Mismatches

« on: January 15, 2010, 12:12:28 pm »

Hi all,

I am studying the human DNA mismatch recognition protein, MutS, which is bound to a G-T mismatch.  The PDBID is 2o8b.pdb.  After extracting the DNA coordinates and analyzing it with 3dna, I get the following base-pair step parameters:

Local base-pair step parameters
    step       Shift     Slide      Rise      Tilt      Roll     Twist
   1 AA/TT     -0.54     -0.56      3.45      4.80     -4.35     38.73
   2 AC/GT      1.04     -0.46      3.47     -1.76      2.29     34.74
   3 CC/GG     -0.09     -0.04      3.17      8.61      5.77     27.01
   4 CG/CG     -0.46      0.75      3.23     -4.45      6.89     35.38
   5 GC/GC     -0.20      0.24      3.45      2.85     -2.55     38.63
   6 CG/TG      ----      ----      ----      ----      ----      ----
   7 GC/GT      3.87      0.83      3.32    -11.26      0.08      6.18
   8 CG/CG      0.16     -0.00      2.69     -0.59      9.40     30.96
   9 GC/GC      0.67     -0.69      3.51      4.51      7.01     29.83
  10 CT/AG     -0.58     -0.42      3.55     -0.60      3.16     36.13
  11 TA/TA      0.06      0.40      3.32      3.45      0.91     39.35
  12 AG/CT      0.63     -0.36      2.88     -6.44      5.81     20.96
  13 GG/CC      0.33     -0.95      3.81      4.06     12.57     33.98

I should point out that step 6 is where the G-T mismatch is located but I don't understand why the parameter values are missing.  In addition, I notice that another output file (bp_step.par) that contains the base-pair step parameters actually has values for the mismatch:

  14 base-pairs
   0  ***local base-pair & step parameters***
       Shear  Stretch  Stagger Buckle Prop-Tw Opening   Shift  Slide    Rise    Tilt    Roll   Twist
A-T    -0.30    0.18    0.82   15.93  -21.58   -1.06    0.00    0.00    0.00    0.00    0.00    0.00
A-T     0.22    0.08    0.03    7.86  -16.61   -8.39   -0.54   -0.56    3.45    4.80   -4.35   38.73
C-G     0.74   -0.12    0.19    1.74   -8.41    4.29    1.04   -0.46    3.47   -1.76    2.29   34.74
C-G    -0.40    0.27   -0.29    8.49  -15.11    7.26   -0.09   -0.04    3.17    8.61    5.77   27.01
G-C    -0.08   -0.04    0.27   18.38   -5.82   -3.77   -0.46    0.75    3.23   -4.45    6.89   35.38
C-G     0.19   -0.11    0.01   11.72  -21.15   -2.89   -0.20    0.24    3.45    2.85   -2.55   38.63
G-T     5.21    0.18    0.31  -41.44   12.48  -69.61   -1.53    1.35    7.27    9.79   65.43   41.15
C-G     0.17   -0.23    0.33  -20.98   -0.21   -5.76    3.87    0.83    3.32  -11.26    0.08    6.18
G-C    -0.12   -0.03    0.39    9.91   -4.28    1.38    0.16   -0.00    2.69   -0.59    9.40   30.96
C-G     0.26    0.06   -0.01    2.86  -12.54    4.36    0.67   -0.69    3.51    4.51    7.01   29.83
T-A     0.70   -0.16    0.47    0.86  -11.85   -2.94   -0.58   -0.42    3.55   -0.60    3.16   36.13
A-T     0.46   -0.21    0.18   -0.01   -9.30   -1.93    0.06    0.40    3.32    3.45    0.91   39.35
G-C    -0.69   -0.09    0.94   18.10  -11.18   -0.17    0.63   -0.36    2.88   -6.44    5.81   20.96
G-C    -1.15   -0.22    0.05   -6.23  -37.33   13.97    0.33   -0.95    3.81    4.06   12.57   33.98


The (shift, slide, rise, tilt, roll) values are essentially identical in both cases with the exception of the missing values for the mismatch.  What do the values in the latter case actually mean and why are they missing in the first case?  What I am interested in is calculating the local curvature around the mismatch (and not the global curvature) but since the first set of base-pair step parameters do not have values then it is not possible to calculate accurate curvature values surrounding the mismatch (since the program that I am using requires the base-pair step parameters as input).  I want to show that although the global curvature is large, the local curvature of the DNA is relatively straight (when compared to, say, straight B-DNA).  I am currently using MADBEND to measure DNA curvature (I generate the necessary base-pair step parameters to be used in MADBEND) and I understand that this isn't a program that you are supporting but I just thought that this would be relevant information.

Any help would be greatly appreciated!  Thank you for your time.

Sean