To make electrostatic surface view of protein using PyMOL, two ways are often suggest. One option is using ABPS to generate the electrostatic map. Here is one nice instruction at PyMOLwiki using ABPS. Another option is using Delphi developed by Barry Honig group to generate the electrostatic map of protein. I am writing a note [...]
[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] Sidechain helper in the cartoon view
Sidechain helper in the cartoon view
Using cartoon view to present the protein secondary structures and tertiary structure is common and we also often see people present some sidechains of particular residues which may be important in some biological roles. In PyMOL, when sidechain atoms are presented in the “sticks mode” with the cartoon*scaffold, we always see the backbone atoms (e.g. http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=609&subd=kpwu&ref=&feed=1
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nmrlearner
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11-13-2011 04:51 AM
[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] pynmr ? an excellent PyMol?s NMR extension
pynmr ? an excellent PyMol?s NMR extension
When I installed PyMol on my iMac using Fink, I found there are some plugins installed already. One of the famous plugin is PDB loader, I believe every one loves it a lot. A new one (at least it’s new to me) is NMR extension written by a Canadian group. Thank you! I’m lovin it http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=301&subd=kpwu&ref=&feed=1
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nmrlearner
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04-02-2011 09:44 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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PyMOL-electrostaic surface view
Linear Mode
