Recipe 4 of 3DNA Nature paper: Questions

[ilibarra]

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

[xiangjun]

Hi Ignacio,

Thanks for your detailed questions regarding recipes #4 in our 2008 3DNA Nature Protocols paper. I am glad to know that you can reproduce recipes #1-3 and 5 without any problem. Check "What's New" item dated 2012-04-25 for switching from Perl to Ruby as the scripting language in 3DNA v2.1.

As mentioned at the very top of "script_h1x_h3y" for recipe #4:

# This script is a bit long, but it is actually quite simple.
# Try to understand exactly how it works, you would qualify as
# an expert 3DNA user!

Recipe #4 should be reproducible as the other ones. The best way to understand the procedures is to duplicate the whole directory to a new location, repeat and check each step as you move along.

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?

The .r3d file is in plain text, so you can view or edit it any way you like, e.g., using vi/emacs. Check Raster3D homepage for details about the .r3d format.

Is this blocview.r3d file the t.r3d file that I should've obtained?

The new Ruby version of 'blocview' generates the file 'blocview.r3d' instead of 't.r3d'. The final composite .r3d file is named '1egk_ok.r3d', which can be loaded directly into PyMOL. Note that the original Perl scripts are still available under $X3DNA/perl_scripts/.

All the scripts are distributed with 3DNA; reading through/between the lines is the most effective way to fully understand what's going on.

HTH,

Xiang-Jun

[ilibarra]

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

[xiangjun]

The 1st line is a comment, while the next two lines define just the resolution of the Raster3D render-ed image. Check .r3d format for details.

In the $X3DNA/config/ directory, there are two files, my_header.r3d (default) and my_header_hres.r3d. Simply copy my_header_hres.r3d to my_header.r3d in the $X3DNA/config/ directory or to your working directory to use the high resolution settings. Alternatively, you can manually edit the .r3d file directly. Moreover, when a .r3d file is loaded into PyMol, the three lines have no influence at all.

Thanks for your posts -- I'm happy to see that you are able to fully verify our reported results.

HTH,

Xiang-Jun

PS: In "3DNA Nature Protocols Paper [vol.3, no.7 (2008), 1213-1227]" dated September 27, 2008, I wrote:

Importantly, in the NP_Recipes subdirectory distributed with 3DNA v2.0,  I have included all scripts, original data files and generated images, so that qualified researchers should be able to reproduce accurately our results without difficulty. Of course, I am more than willing and would be quick to address any reproducibility issues you may have. Repeatability is one of the basic requirements of a published scientific work, yet in this "high-throughput" / "big science" age reproducibility is sort of becoming a luxury.

In 3DNA v2.1, I've updated the scripts to ensure continuous reproducibility of our 2008 Nature Protocols paper.