RigiMOL is a feature only available in incentive PyMOL, not in open source built PyMOL. The following two short (very short) youtube videos are made by the example script provided at PyMOLWiki (script link at here). The demo script is also pasted at here: ==================================== # get open and closed conformation of adenylate kinase fetch [...]
[Question from NMRWiki Q&A forum] How do you list H-bonds in pymol?
How do you list H-bonds in pymol?
Hi there,
I am trying to compare the H-bonds in two NMR strcutures. So, I need to calculate H-bonds with a cutoff 2.5 and angle 35 angestrom that are availbale in 10 structures out of 20. I run list_hbonds.py as below:
list_hb, selection1, cutoff=2.5, angle=35
but it doesn not meet what I want. I want to look at inter and intra H-bonds (between two complexes of the protein and in each chain, too).
nmrlearner
News from other NMR forums
0
04-05-2013 11:03 PM
[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
Go to KPWU blog to read complete post.
nmrlearner
News from NMR blogs
0
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
Go to KPWU blog to read complete post.
nmrlearner
News from NMR blogs
0
08-21-2012 02:05 PM
[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
Go to KPWU blog to read complete post.
nmrlearner
News from NMR blogs
0
06-26-2012 06:27 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
Go to KPWU blog to read complete post.
nmrlearner
News from NMR blogs
0
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
Go to KPWU blog to read complete post.
nmrlearner
News from NMR blogs
0
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
Go to KPWU blog to read complete post.
nmrlearner
News from NMR blogs
0
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
Go to KPWU blog to read complete post.
Morphing movie using RigiMOL/PyMOL
Linear Mode
