Messages

1

General discussions (Q&As) / Re: Get major/minor grooves from structure with broken linkages

« on: August 14, 2017, 10:58:11 am »

I have been able to extract the groove values by running Curves+. I guess that's a solution for now .

Thanks,
Ignacio

2

General discussions (Q&As) / Get major/minor grooves from structure with broken linkages

« on: August 14, 2017, 05:43:55 am »

Dear Dr. Lu,

I have a PDB entry from which I'd like to get groove parameters. However, it seemst that because the DNA chains are not completely connected during the find_pair routine, the analyze routine cannot calculate the parameters. I have run this PDB entry as a whole, and also extracting the DNA chains I'm interested (please find them both attached in this post).

# command
find_pair 4xrs_dna.pdb

    2         # duplex
    8         # number of base-pairs
    1     1    # explicit bp numbering/hetero atoms
    1    30   1 #    1 + ....>L:...2_:[.DT]T-**+-A[.DA]:..34_:M<....   7.99   1.08  26.53  10.95  11.47
    4    28   0 #    2 | ....>L:...5_:[.DA]A-**--T[.DT]:..32_:M<....   5.43   0.84  27.23  10.31   8.48
    5    26   9 #    3 x ....>L:...6_:[.DC]C-**--T[.DT]:..30_:M<....   2.42   0.92  25.10  10.44   4.51
    8    24   0 #    4 | ....>L:...9_:[.DG]G-----C[.DC]:..28_:M<....   1.94   1.69  62.83  10.24   5.47
    9    23   9 #    5 x ....>L:..10_:[.DA]A-----T[.DT]:..27_:M<....   0.79   0.44  52.85   8.67  -0.69
   12    20   1 #    6 + ....>L:..13_:[.DA]A-**+-T[.DT]:..24_:M<....   1.12   0.86  61.41   8.40   4.90
   14    18   0 #    7 | ....>L:..15_:[.DT]T-**+-A[.DA]:..22_:M<....   3.48   0.53  63.53   9.27   7.71
   15    16   0 #    8 | ....>L:..16_:[.DG]G-**+-T[.DT]:..17_:L<....   7.51   1.27  52.73   6.84  11.70
##### Base-pair criteria used:     4.00     0.00    15.00     2.50    65.00     4.50     7.80 [ O N]
##### 6 non-Watson-Crick base-pairs, and 5 helices (2 isolated bps)
##### Helix #1 (1): 1
##### Helix #2 (2): 2 - 3  ***broken O3' to P[i+1] linkage***
##### Helix #3 (2): 4 - 5
##### Helix #4 (1): 6
##### Helix #5 (2): 7 - 8  ***broken O3' to P[i+1] linkage***

Is the main reason for this structure not being completed the broken linkages? is it possible to fix the linkages with 3DNA or increase the distance threshold to tolerate them, in order to recover the al the base pairs and then calculate the grooves?

At the moment, the groove parameters are empty.

(output from analyze 4xrs_dna.inp. Only eight base pairs from the DNA-duplex are recovered and shown).

Minor and major groove widths: direct P-P distances and refined P-P distances
   which take into account the directions of the sugar-phosphate backbones

   (Subtract 5.8 Angstrom from the values to take account of the vdw radii
    of the phosphate groups, and for comparison with FreeHelix and Curves.)

Ref: M. A. El Hassan and C. R. Calladine (1998). ``Two Distinct Modes of
     Protein-induced Bending in DNA.'' J. Mol. Biol., v282, pp331-343.

                  Minor Groove        Major Groove
                 P-P     Refined     P-P     Refined
   1 TA/TA       ---       ---       ---       ---
   2 AC/TT       ---       ---       ---       ---
   3 CG/CT       ---       ---       ---       ---
   4 GA/TC       ---       ---       ---       ---
   5 AA/TT       ---       ---       ---       ---
   6 AT/AT       ---       ---       ---       ---
   7 TG/TA       ---       ---       ---       ---

Thank you for any feedback or suggestion,

Ignacio

P.S. This is a similar post that reports a similar warning.
http://forum.x3dna.org/general-discussions/this-structure-has-broken-o3'-to-p(i1)-linkages/

3

Feature requests / Re: Binary for Mac 10.5.8 (2 x 2.8 Quad-Core Intel Xeon)

« on: March 19, 2014, 12:38:44 am »

Thanks for the time and the answer. It has helped me.

I have compiled v2.0 without problems before writing this post. However, the function I am interested is "mutate_bases". I am concerned it is available for easier use since v2.1.
http://forum.x3dna.org/programs/mutate_bases/

I will run a virtual machine or run mutate_bases with v2.1 somewhere else. I have no problems with this, but I wanted primarily to do everything in the same computer.

4

Feature requests / Binary for Mac 10.5.8 (2 x 2.8 Quad-Core Intel Xeon)

« on: March 14, 2014, 03:26:46 pm »

I have installed 3DNA in a Mac 10.5.8 (2 x 2.8 Quad-Core Intel Xeon)

I have checked the environment variables. They are OK.

bolt:bin ignacio$ echo $X3DNA
/Users/ignacio/Software/x3dna-v2.1
bolt:bin ignacio$ echo $PATH
/Users/ignacio/Software/x3dna-v2.1/bin

However, when executing the test script (or any), I got the following error:

bolt:bin ignacio$ ./find_pair -h
dyld: unknown required load command 0x80000022
Trace/BPT trap
bolt:bin ignacio$ ./mutate_bases
dyld: unknown required load command 0x80000022
Trace/BPT trap

I would like to ask a version of 3DNA for this architecture. If the error was reported somewhere else in this site (I did not find it at the moment) I would like to be referred to the post.

Thanks in advance,

Ignacio Ibarra

5

General discussions (Q&As) / Re: Datasets and scripts for reproducing Figure 5 of the 3DNA NAR03 paper

« on: September 03, 2012, 10:44:45 pm »

Thank you very much for the fast answers to the questions of this forum

6

General discussions (Q&As) / Datasets and scripts for reproducing Figure 5 of the 3DNA NAR03 paper

« on: August 31, 2012, 05:05:06 pm »

The scheme of classifying a dinucleotide step into A-, B- or TA-DNA form is described in the 2003 NAR paper. More specifically, it is based on Zp and Zp(h); see Figure 5(c) linked below. For example, if Zp > 1.5 Å, then it is taken as A-DNA.



Per your request, listed below is the exact definition for A-, B- and TA-DNA, as excerpted from 3DNA source code. Note the "sanity check" at the beginning; the empirical criteria try to ensure a right-handed duplex consisting of Watson-Crick bps and with reasonable geometry. Also bear in mind that the classification is intended to be indicative rather than conclusive.

Code: [Select]

if (dval_in_range(mtwist, 10.0, 60.0)  /* over-all twist average */
    && WC_info[i] && WC_info[i + 1]  /* WC geometry */
    && dval_in_range(twist_rise[i][1], 10.0, 60.0)  /* right-handed */
    && dval_in_range(twist_rise[i][2], 2.5, 5.5)  /* Rise in range */
    && dval_in_range(aveS[i][1], -5.0, -0.5)  /* Xp */
    && dval_in_range(aveS[i][2], 7.5, 10.0)  /* Yp */
    && dval_in_range(aveS[i][3], -2.0, 3.5)  /* Zp */
    && dval_in_range(aveH[i][1], -11.5, 2.5)  /* XpH */
    && dval_in_range(aveH[i][2], 1.5, 10.0)  /* YpH */
    && dval_in_range(aveH[i][3], -3.0, 9.0)) {  /* ZpH */
    if (aveS[i][3] >= 1.5)  /* A-form */
        strABT[i] = 1;
    else if (aveH[i][3] >= 4.0)  /* TA-form */
        strABT[i] = 3;
    else if (aveS[i][3] <= 0.5 && aveH[i][1] < 0.5)  /* B-form */
        strABT[i] = 2;  /* aveS[i][3] < 0.5 for C-DNA #47 */
}
HTH,

Xiang-Jun

I'd like to ask about the DNA set used for the analysis that is presented in Fig 5. in the NAR 2003 paper. Are those structures previously classified as A, B and TA DNA by other means (?) before doing the Zp and Zp(h) calculations to confirm their differences? Where can I look for the structures which were used? (I guess it is somewhere in reference 81, Patikoglou,G.A. et al (1999))

Thanks for the comments

Ignacio

7

General discussions (Q&As) / Re: Recipe 4 of 3DNA Nature paper: Questions

« on: July 01, 2012, 01:23:53 am »

Thanks for the fast answer!

Now I have done the example completely. It is working and I learned the format syntax in Raster3D. Thanks!

One last thing I would like to ask is:

I observe that the resolution of the final picture, "1egk_ok.png" after running the script from scratch is different with respect to the one that is in the R4 example folder by default. The sizes are 202.5kB and 1.2MB, respectively. I have backtracked up to the blocview.r3d file, and comparing them (the one that is by default and the one created from zero) I found the following difference:

ignacio@ignacio:~/Downloads/3DNA_EXAMPLES/R4_4way_junction$ diff blocview.r3d ../R4_4way_junction_test/.
1,3c1,3
< 3DNA v2.0 (2007-08-20, by Dr. Xiang-Jun Lu; 3dna.lu@gmail.com)
< 160  160            tiles in x, y
< 16   16             pixels (x, y) per tile
---
> 3DNA v2.1 (2012-05-01, by Dr. Xiang-Jun Lu; http://x3dna.org/)
> 80  80            tiles in x, y
> 8   8             pixels (x, y) per tile


The blocview.r3d file that is created in the R4 recipe have differences in those three lines. I guess that it was dependent of one of the files that is also inside the folder, but which is not stated explicitly during the recipe script. Am I right? I interpret that it is the rendering parameter the one that was changed, and the version of 3DNA that is used.

Cheers,
Ignacio

8

General discussions (Q&As) / Recipe 4 of 3DNA Nature paper: Questions

« on: June 30, 2012, 02:16:32 am »

I have done the Recipes 1-3 and 5 with no problems using the "x3dna-v2.1beta" version of 3DNA. I have realized some particular things have changed in the command syntax, but I figured them out.

For the recipe number 4, I have several doubts

First, in this section:
"
(vii) Rename (‘\mv’) the Raster3D file ‘poc_haxis.r3d’ into file ‘h1x.r3d’ (line 13) and manually modify ‘h1x.r3d’, by
uncommenting (i.e., selecting) the cylinder scenes based on the phosphorus atoms, changing the color to red
(by modifying its RGB color components). The updated Raster3D file is now called ‘h1x_ok.r3d’. Compare the two files
(‘h1x.r3d’ and ‘h1x_ok.r3d’) to see the difference, for example, use the Unix command diff.
"

I created the file "h1x.r3d" (Recipe 4, line 13) changing the name of poc_haxis.r3d:

"mv poc_haxis.r3d h1x.r3d"

Now, I got lost reading the file as text. I see several numbers but I am not sure what the cylinder scenes are.

How should I open the .r3d file to edit it? Is there a particular command or with a text editor like vi should be enough?


For now, I just jumped this step and then, instead of doing this command declared in line 17

"cat t.r3d transparent.r3d h1x_ok.r3dh3y_ok.r3d > 1egk_ok.r3d"

I did

"cat blocview.r3d transparent.r3d h1x.r3d h3y.r3d > 1egk_ok.r3d"

The stated file blocview.r3d was created as output in line 16 (blocview routine), and I am using it because it did not create a file called t.r3d.

Is this blocview.r3d file the t.r3d file that I should've obtained? I am assuming that it was a change in the output file name with the new version, and maybe I am wrong.

I am using the transparent.r3d file that is in the following path
"/usr/share/raster3d/materials/transparent.r3d"

Finally, after doing all this I obtained two image files, after the last command, and an empty msgfile (0 bytes). None of the images is called like the final .png that it was declared, and they seem to be temps files of the last routine (x3dna_r3d.avs and temp_r3d.png).

I have attached everything in this thread if someone wants to see the files. Also, a "run.sh" script is inside, with a transcript of the commands that define the Recipe 4, with my modifications already mentioned.

Thanks for the feedback.

Cheers,
Ignacio

9

General discussions (Q&As) / Re: side_view.dat rotate_mol NO rotation

« on: June 29, 2012, 07:11:29 pm »

Okay.

With side_view.dat file it seems to be working. My problem is solved  .

Anyway, I can't recognize differences between both side_view.dat files. In this file, I have typed all the characters, while in the first one I copied the texts from the .pdf paper. I think that is the reason of the difference during execution.

Cheers,
Ignacio

10

General discussions (Q&As) / Re: side_view.dat rotate_mol NO rotation

« on: June 29, 2012, 06:58:23 pm »

Using the Recipe 02, I see that the command works. I will check in details the recipe 01 to see what is different. In the meantime, I leave the input files that I am using for that particular command

11

General discussions (Q&As) / side_view.dat rotate_mol NO rotation

« on: June 29, 2012, 06:38:49 pm »

Hello,

I am using the following command (as detailed in the Recipe 01 of the Nature 3DNA paper)

"rotate_mol -r=side_view.dat propeller_mg.alc propeller_sv.alc"

side_view.dat has the following text written, in two lines

"
by rotation y –30
by rotation x 20
"

I receive as output:
"wrong <by rotation> format"

I have checked many things (tabs, spaces number) with the same results. Also writing "byrotation" or just "rotation" as keyword gives me an output file but with no rotations. I obtain the message "NO rotation applied to the structure", and the final of the recipe (.fig) is not rotated as it is explained in expected results.

I would like to know if there is something that I am doing wrong with this file. I have everything else until that step working properly

Cheers,
Ignacio