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Author Topic: blocview  (Read 5915 times)

Offline ahudson

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blocview
« on: September 20, 2014, 04:04:50 pm »
Hi,

I'm trying to use blocview to generate images of RNA structures I have, and I was wondering if you had to do anything special to create images like the ones in the DSSR manual. Specifically, I had in mind the image on the cover of the manual and the image in Figure 1A on page 11 of the manual. Those images seem to have a bit more depth to them than the example image included with the blocview blog post.

Alex

Offline xiangjun

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Re: blocview
« Reply #1 on: September 20, 2014, 07:38:01 pm »
Hi Alex,

The blocview script in 3DNA works by first generating a .r3d file, which can then be fed into render of Raster3D (by default) or PyMOL. The sample image on the blog page was rendered with Raster3D. The two RNA images (for 1ehz and 1msy) you referred to in the DSSR User Manual were ray-traced with PyMOL, and they appear to have a better sense of depth.

There are many parameters in PyMOL you can play with. Specifically, the .pml file for the tRNA 1ehz image is as below, assuming the blocview generated .r3d file is named 1ehz.r3d:

Code: [Select]
load 1ehz.r3d

bg_color white
set depth_cue=0
set ray_trace_fog=0

set label_size, 14
set label_outline_color, 1
set label_color, green
set label_position, [0, 0, 10]

set antialias = 1

set stick_radius = 0.12
set sphere_scale, 0.16, *
show sticks
show spheres
 
# color carbon white as in RasMol
util.cbaw
hide everything, solvent

zoom complete=1
ray 2400, 2400
png 1ehz-pymol.png

HTH,

Xiang-Jun

 

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.