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Hi Xiang-Jun,
In using blocview I know that the radius of the backbone tube which traces the phosphate atoms can be changed in the last line of the $X3DNA/config/col_chain.dat file.
Nonetheless I would also like to change the radius of the sticks representing the sugar-phosphate backbone bonds.
I can do this manually by altering the resulting .r3d files, say, if one of these bond specifications as a cylinder in raster3D is:
3
-10.965 -18.757 -1.704 0.160 -9.568 -18.592 -1.909 0.160 1.000 1.000 0.000
I can change the 0.160 value in the fourth and eight fields to whichever radius I want.
I was wondering if there's a file where this parameter can be changed in an easier way.
Thanks,
Mauricio
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Hi Mauricio,
Nice to see you again on the 3DNA Forum!
I would also like to change the radius of the sticks representing the sugar-phosphate backbone bonds.
The default radius of the sticks is set via the r3d_atom -r=0.16 option in the blocview script. See the excerpt below:
# color nucleic-acid base/sugar by residue type
Utils.run_cmd("#{$x3dna}r3d_atom -ncz -r=0.16 tb.pdb #{$temp_r3d} #{$msg}")
Utils.append_r3dfile(opts[:r3dfile], $temp_r3d)
So you may change the radius 0.16 to your preferred value.
Alternatively (and preferably), you may want to give DSSR a try. DSSR has integrated blocview as a command-line option, and employes PyMOL for rendering. See the DSSR User Manual (http://docs.x3dna.org/dssr-manual.pdf) for more details.
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