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Questions and answers > General discussions (Q&As)

blocview

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mauricio esguerra:
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:


--- Code: ---3
  -10.965  -18.757   -1.704    0.160   -9.568  -18.592   -1.909    0.160    1.000    1.000    0.000

--- End code ---

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

xiangjun:
Hi Mauricio,

Nice to see you again on the 3DNA Forum!


--- Quote ---I would also like to change the radius of the sticks representing the sugar-phosphate backbone bonds.
--- End quote ---

The default radius of the sticks is set via the r3d_atom -r=0.16 option in the blocview script. See the excerpt below:


--- Code: Ruby ---        # 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 for more details.

HTH,

Xiang-Jun

 

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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.