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Author Topic: blocview  (Read 124 times)

Offline mauricio esguerra

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blocview
« on: June 20, 2018, 08:44:54 am »
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: [Select]
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


Offline xiangjun

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Re: blocview
« Reply #1 on: June 20, 2018, 01:21:05 pm »
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.

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
  1.         # color nucleic-acid base/sugar by residue type
  2.         Utils.run_cmd("#{$x3dna}r3d_atom -ncz -r=0.16 tb.pdb #{$temp_r3d} #{$msg}")
  3.         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

 
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.