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Author Topic: Rendering Images of RNA  (Read 5529 times)

Offline Pablo Ricardo Arantes

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Rendering Images of RNA
« on: April 30, 2013, 08:31:18 pm »
Hello!

I work with RNA, and first I would like to thank for dssr program. It's excellent program. Congratulations!!
I would like to know, how can I create a picture with texture on ribbon. If you look at the picture attached, you understood what I'm saying.
I can create images but I can't make a texture on ribbon at Pymol. In picture attached I highlighted what I need.

Thanks!

Best regards.

Pablo Arantes



Offline xiangjun

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Re: Rendering Images of RNA
« Reply #1 on: April 30, 2013, 09:14:06 pm »
Hi Pablo Arantes,

Thanks for trying out DSSR and your kind words about it! Note that DSSR is still in beta, and I welcome user feedbacks to guide further refinements of the software.

Regarding the texture on ribbon rendered with PyMOL, I understand what you mean from the attached figures. I honestly do not know how it comes out that way when a blocview generated .r3d file in fed into PyMOL -- I've actually thought that it is an artifact!

I will try to reproduce the 1msy schematic image with texture in ribbon, and post back details for your reference (hopefully by tomorrow).

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

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Offline xiangjun

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Re: Rendering Images of RNA
« Reply #2 on: May 01, 2013, 10:04:33 pm »
Hi Pablo Arantes,

Here are the details I used to generate the 1msy schematic image with texture on ribbon. I am using PyMOL v1.5.0.3 on Mac OS X, and 3DNA v2.1 as currently downloadable from the site.

Code: [Select]
# download 1msy.pdb from RCSB PDB; note the -r option to specify the output file "1msy.r3d"
blocview -r 1msy.r3d 1msy.pdb

# run pymol from command line with script "1msy.pml" (see below)
pymol -qc 1msy.pml

The content of "1msy.pml" (also attached) is as below:
Code: [Select]
load 1msy.r3d
bg_color white
set depth_cue=0
set ray_trace_fog=0
ray 1200,1200
png 1msy.png, dpi=300

Here are the three attachments: 1msy.r3d; 1msy.pml; 1msy.png

As you see, I've done nothing special with PyMOL rendering to get the 'texture'. I'm interested in knowing why you're not having it. Maybe it is related to some PyMOL settings.

Xiang-Jun
« Last Edit: May 01, 2013, 10:16:46 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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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.