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Questions and answers => General discussions (Q&As) => Topic started by: Obliv111 on July 29, 2007, 11:45:54 am

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Title: Generating Images with 3DNA
Post by: Obliv111 on July 29, 2007, 11:45:54 am

Hello,

I would like to make images of the NDB structures BD0054 and PD0254.  The images must be consistent with the color-coding of the backbone ribbons, i.e., Strand I must be the same color in both images and Strand II must be a different color but also the same in both images.  Can you tell me how to do this?

Thank you.

Title:
Post by: xiangjun on July 30, 2007, 12:48:15 am

Hi,

The chain color is controlled by file "col_chain.dat" under directory $X3DNA/BASEPARS in 3DNA v1.5. It is copied below:

Code: [Select]

# Coloring scheme for chains in "blocview" generated images.
# This list contains one-letter chain-ID and corresponding color name
#      which should be one of MolScript's 164 pre-defined names stored
#      in file "mcolname.dat". Otherwise, the default color corresponding
#      to "*" at the end is used.
# 0-9 are assigned the same color as A-J
# Users might change colors here or add new chains and their colors
A       red
B       yellow
C       yellow
D       cyan
E       blue
F       brown
G       violet
H       wheat
I       pink
J       bisque
K       khaki
L       magenta
M       peru
N       plum
O       green
P       tan
Q       tomato
R       orange
S       turquoise
T       salmon
U       blanchedalmond
V       firebrick
W       blueviolet
X       darkgreen
Y       darkturquoise
Z       orangered
0       red
1       yellow
2       lawngreen
3       cyan
4       blue
5       brown
6       violet
7       wheat
8       pink
9       bisque
*       goldenrod

# protein by_chain [default] or a specific color
protein   purple

# nucleic acid by_chain [default] or a specific color [coil_radius]
nucleic_acid    by_chain  0.8


The file BD0054 has chains A & B for DNA, PD0254 has chains B & C, so you should now understand the reason for the different coloring of DNA in these two structures (e.g., in the NDB website).

Simply change the color name for a specific chain to you liking will do the trick. You might want to copy the file "col_chain.dat" to your current working directory for local effect instead of changing it under $X3DNA/BASEPARS for global effect (see also http://rutchem.rutgers.edu/~xiangjun/3D ... #find_pair (http://rutchem.rutgers.edu/~xiangjun/3DNA/faq.html#find_pair)).

HTH,

Xiang-Jun

Title:
Post by: Obliv111 on July 30, 2007, 11:02:43 pm

Thanks, this makes a lot of sense.

How do I actually generate the image?  I have downloaded 3DNA for Windows and am able to access it through cygwin.  What are the commands to generate an image?

Thanks again.

Title:
Post by: xiangjun on July 30, 2007, 11:23:51 pm

You use the Perl script "blocview" -- it calls Molscript, Raster3D, and ImageMagick, so you also need to have them installed (they are readily available from the internet).

Type "blocview -h" for help info, and check the script to understand how it works.

Once everything is properly installed, to get the image as in the NDB is trivial. E.g., for BD0054 (1jgr.pdb1), you just need to type:

Code: [Select]

blocview -i=BD0054.jpg 1jgr.pdb1
display BD0054.jpgor

Code: [Select]

blocview -d 1jgr.pdb1
with a default image name "t.jpg"

HTH,

Xiang-Jun

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University