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General discussions (Q&As) /
« 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:
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).
HTH,
Xiang-Jun
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).
HTH,
Xiang-Jun