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 Wiki
[NMR images] making NMR invaluable as a
http://www.chem.duke.edu/~wwarren/fig83.jpg
http://www.chem.duke.edu/~wwarren/nmr.php
20/02/2012 3:31:02 PM GMT
making NMR invaluable as a
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nmrlearner
NMR pictures
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02-20-2012 03:25 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
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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
Go to KPWU blog to read complete post.
nmrlearner
News from NMR blogs
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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
Go to KPWU blog to read complete post.
nmrlearner
News from NMR blogs
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07-10-2011 07:23 AM
[KPWU blog] Making Ramachandran plot ?II
Making Ramachandran plot ?II
Long time ago, I made a blog article at here to make a record where I can go back to dig information of Ramachandran plot. But the ranges used in the Ramachandran plot are a bit out of date. The Richardson group has a publication in 2003*(Structure validation by Calpha geometry: phi,psi and Cbeta deviation http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=349&subd=kpwu&ref=&feed=1
Go to KPWU blog to read complete post.
nmrlearner
News from NMR blogs
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04-20-2011 02:51 AM
[KPWU blog] [NMRPipe]?making a 3D cube
?making a 3D cube
On Feb 18th, an user asked whether there are ways to make a 3D cube of NMR data at the NMRPipe discussion group at Yahoo. Frank Delaglio, the author of NMRPipe, provided a very very nice script to generate the cube. The script is pasted in this post and user can copy it, save it http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=329&subd=kpwu&ref=&feed=1
Go to KPWU blog to read complete post.
Site-specific labeling of nucleotides for making RNA for high resolution NMR studies
Abstract Escherichia coli (E. coli) is a versatile organism for making nucleotides labeled with stable isotopes (13C, 15N, and/or 2H) for structural and molecular dynamics characterizations. Growth of a mutant E. coli strain deficient in the pentose phosphate pathway enzyme glucose-6-phosphate dehydrogenase (K10-1516) on 2-13C-glycerol and 15N-ammonium sulfate in Studier minimal medium enables labeling at sites useful for NMR spectroscopy. However, 13C-sodium formate combined with 13C-2-glycerol in the growth media adds labels to new positions. In the absence of labeled formate, both C5 and...
PyMOL?making movies
Linear Mode
