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Author Topic: Blocview with .pdb output?  (Read 4887 times)

Offline zenita

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Blocview with .pdb output?
« on: March 24, 2016, 07:52:25 am »
Dear Dr. Xiang Jun,

Is it possible to get a .pdb output from 3dna blocview command or dssr cartoon block option?

I found your article which mentioned that with 3dna it is possible to get .alc file which can be converted to .pdb.
http://x3dna.org/highlights/rectangular-block-expressed-in-pdb-format

However, when I check with 3dna v2.3 , it seems it will only give .png or .r3d output? With dssr I also got only .r3d output.

When I open the r3d file output in pymol, I find that pymol cannot do much modification on it (change color etc) so I'm hoping to get .pdb file.

Thank you,
Zenita

Offline xiangjun

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Re: Blocview with .pdb output?
« Reply #1 on: March 24, 2016, 11:13:49 am »
Quote
Is it possible to get a .pdb output from 3dna blocview command or dssr cartoon block option?

The blocview or DSSR cartoon-block images are in Raster3D .r3d format, which can be rendered with PyMOL. The various components in a .pdb file are converted to .r3d to show the backbone ribbons or the solid blocks. So, the answer is no because the .r3d format is required for the solid blocks.

Quote
I found your article which mentioned that with 3dna it is possible to get .alc file which can be converted to .pdb.
http://x3dna.org/highlights/rectangular-block-expressed-in-pdb-format

PyMOL does not recognize the .alc format, and Jmol support for .alc was added upon my request. So to facilitate the visualization of base rectangular blocks from 3DNA, I added the conversion from .alc to .pdb using explicit CONNCT records. That's what the blogpost you referred to is about.

Quote
However, when I check with 3dna v2.3 , it seems it will only give .png or .r3d output? With dssr I also got only .r3d output.

The .r3d format is the source from which the .png file is generated with render in Raster3D or PyMOL. Have a look of the blocview script, you will see how the pieces are tied together.

With DSSR, I've deliberately removed any direct dependency on third-party tools. So you get a .r3d output, which you can load into PyMOL and combined with other powerful PyMOL features. Did you know that Thomas Holder has written a PyMOL plugin to automate the process? See "Dssr block" and my blogpost linked therein.

Quote
When I open the r3d file output in pymol, I find that pymol cannot do much modification on it (change color etc) so I'm hoping to get .pdb file.

With .r3d, you indeed cannot do much in PyMOL other than changing some rendering options (e.g., light, fog etc). However, the text file $X3DNA/config/raster3d.par contains configurations for the coloring of the base blocks, as shown below:

Code: [Select]
1.000   0.000   0.000    # A red            [255 0   0]
1.000   1.000   0.000    # C yellow         [255 255 0]
0.000   1.000   0.000    # G green          [0   255 0]
0.000   0.154   0.000    # I dark green     [0   100 0]
0.000   0.000   1.000    # T blue           [0   0   255]
0.000   1.000   1.000    # U cyan           [0   255 255]
0.100   0.100   0.100    # X
1.000   1.000   1.000    # fill color white [255 255 255]

In DSSR, the coloring of the base blocks are fixed right now. However, other components can be easily manipulated in PyMOL.

If you can provide details on what you want to achieve, I may be able to offer more concrete help.


Along the line, there is a short Perl script $X3DNA/perl_scripts/block_atom that combines base blocks with atomic representation.

HTH,

Xiang-Jun
« Last Edit: March 24, 2016, 02:57:45 pm by xiangjun »

Offline xiangjun

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Re: Blocview with .pdb output?
« Reply #2 on: March 30, 2016, 04:27:50 pm »
Quote
When I open the r3d file output in pymol, I find that pymol cannot do much modification on it (change color etc) so I'm hoping to get .pdb file.

As a follow-up, I've added the --block-color option to DSSR so one can easily change rendered colors for the base blocks. Some examples,

Code: [Select]
# to make A blue, G red, and the minor groove edge gray
x3dna-dssr -i=1msy.pdb --block-color='A blue, G red, minor gray'
# to make every base block green
x3dna-dssr -i=1msy.pdb --block-color='N green'
# specify color using rgb in range [0, 1] or [0, 255]
x3dna-dssr -i=1msy.pdb --block-color='N 0 1 0'
x3dna-dssr -i=1msy.pdb --block-color='N [0 1 0]'

I've just updated DSSR (v1.5.2-2016apr02) on the download page, intended to be released on April 2. This new option may fit your needs.

Xiang-Jun

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.