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. *
[KPWU blog] [PyMOL] contact map (CMView)
contact map (CMView)
In PyMOL Wiki, there is a “contact map visualizer” plugin providing users to inspect the protein intramolecular contacts. However, this plugin requires “PyGame”, “Tkinter”, “PIL (python image library)” and most importantly, Gromacs! I used Fink (Mac OSX 10.6.8) to successfully install Gromacs 4.1 but Fink reported problems while installing pygame. So I can generate xpm http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=727&subd=kpwu&ref=&feed=1
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nmrlearner
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06-26-2012 06:27 PM
[KPWU blog] [PyMOL] gradient background color
gradient background color
Starting at *PyMOL 1.4, *single color for the background is no longer the only choice. By using 3 PyMOL commands, the gradient background color can be easily shown. The only thing users have to know is that command “ray” doesn’t support this gradient color yet. So if you type “ray” in the pymol terminal , http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=619&subd=kpwu&ref=&feed=1
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nmrlearner
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11-15-2011 11:36 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
[NMR software blog] iPad
iPad
There are too many reasons why any wise guy will never write a program to process or visualize NMR spectra on the iPad. What's the iPad? A small, light-weight device that you can use to read books and newspapers, watch pictures and movies, hear music, play games. It's a machine to enjoy contents created by some other means. If you realize this, you conclude that the iPad comes ready to watch NMR spectra as well, provided that those spectra are saved as PDF.
I think that one day tablets will substitute the PC as we know it today. That day tablets will have evolved from the iPad to...
nmrlearner
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07-02-2011 05:30 PM
[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
Go to KPWU blog to read complete post.
PyMOL on the iPad
Linear Mode
