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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) / 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.

3

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.

4

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

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

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

5

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

6

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

7

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

8

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

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