Saw a post at recent Pymol mailing list and found the nice example of “spectrumany” at PymolWiki. Here is the example I created using “spectrumany” to show customized spectral colors of the example protein TBEV envelope protein “PDBV entry: 1SVB”. By using the built-in command “spectrum”, one can color the envelope protein in 2 or [...]
[KPWU blog] [PyMOL] grid mode
grid mode
It is often that we compare different proteins and want to show all aligned proteins in one time. One popular way shown in scientific papers is to superimpose all structures, however it shows an overlapped “tangle”. *Sometimes such way doesn’t provide a good view for reader. I am going to show you the “grid_mode” provided http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=771&subd=kpwu&ref=&feed=1
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nmrlearner
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08-27-2012 01:58 AM
[KPWU blog] PyMOL on the iPad
PyMOL on the iPad
PyMOL mobile app for iPad released today as posted by PyMOL maintainer at PyMOL mailing list. Please go to “http://pymol.org/mobile” to see details. Or directly go iTunes store to download this App. *http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=759&subd=kpwu&ref=&feed=1
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nmrlearner
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08-21-2012 02:05 PM
[KPWU blog] [PyMOL] different colors of nucleic acid rings
different colors of nucleic acid rings
The image above can be drew followed by steps in*my earlier post, which shows single color of the nucleotide rings and bonds. I saw a discussion list at PyMol forum today that an user requested a way to display different colors of the nucleotide rings. Below is the example image I tested (using PDB: 2WCC). http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=711&subd=kpwu&ref=&feed=1
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nmrlearner
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05-24-2012 05:54 PM
[KPWU blog] [PyMOL] DNA?example II
DNA?example II
Follow up previous post, here shows several modes available in PyMOL to display the ribbon/chain of DNA/RNA. Example molecule: B-form DNA PDB code: *2L8Q Running version, PyMOL 1.3 (x11 version on MacOS 10.6) The previous version use “oval” to show the ribbon of DNA. Here are some other ways to show the ribbon: 1. default http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=446&subd=kpwu&ref=&feed=1
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nmrlearner
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07-28-2011 11:40 PM
[KPWU blog] [PyMOL] example of DNA
example of DNA
Several private emails request me to show some examples of DNA/RNA using PyMOL. I am not familiar with commands related to nucleic acids in PyMOL because I never have chance to study DNA/RNA. I made some posts few years ago just for fun. Here is a step-by-step re-cap I make followed by our old post. http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=429&subd=kpwu&ref=&feed=1
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nmrlearner
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07-26-2011 11:22 PM
[KPWU blog] [PyMOL] use of ?ray_trace_mode?
use of ?ray_trace_mode?
I do like a command called “ray_trace_mode” in PyMOL because different modes can generate different light and color effects on the structure I want to express to readers/students. Here is a quick examples of the effect on different modes. The structure I use at here is LolA which PDB code is 1UA8. 1. ray_trace_mode 0 http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=407&subd=kpwu&ref=&feed=1
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nmrlearner
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07-10-2011 07:23 AM
[KPWU blog] PyMOL?making movies
PyMOL?making movies
I found several good online tutorials of making movies using PyMOL and provide the links at here. *I should make some examples by my own next time. PyMOL tips and tricks at Dept. Biochemistry, University of Cambridge How to make a movie PyMOL at Youtube Movie school #6 at PyMOL Wikihttp://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=319&subd=kpwu&ref=&feed=1
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nmrlearner
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04-09-2011 12:17 AM
[KPWU blog] [PyMOL] give your protein a box!
give your protein a box!
Here is a nice script to draw a minimu bounding box of your target PDB. Author: Jason Vertrees Example of 2GB1, using stereo view: usage: run PATH/drawMinBoundingBox.py drawMinBoundingBox.py 2GB1, 3, r=0.3, g=0.3, b=0.3 ====== drawMinBoundingBox ]]]] Download this script at pymolwiki.http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=200&subd=kpwu&ref=&feed=1
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