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 But the ranges used in the Ramachandran plot are a bit out of date.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 [...]
[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] Ramachandran space of Glycine and Proline
Ramachandran space of Glycine and Proline
The following two plots are made according to the statistical values provided by the Richardson group. I download the KINEMAGE format of Glycine and Proline. Inside the two files, core and allowed regions are defined and can be extracted to make my own Ramachandran plot. The defined core and allowed regions are also shown in http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=397&subd=kpwu&ref=&feed=1
Go to KPWU blog to read complete post.
nmrlearner
News from NMR blogs
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06-18-2011 03:04 AM
[KPWU blog] Examples of Ramachandran plots of residues in helix, strand or coil regions
Examples of Ramachandran plots of residues in helix, strand or coil regions
Few weeks ago, I posted a blog that provides a newer collected/organized dataset for the torsional angles of proteins. I played around and try to use GnuPlot 4.4 to make my own Ramachandran plots. Here are three examples of the residual Ramachandran space regarding to the helical, extend or coil regions. I used STRIDE to http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=372&subd=kpwu&ref=&feed=1
Go to KPWU blog to read complete post.
nmrlearner
News from NMR blogs
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05-10-2011 07:07 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.
nmrlearner
News from NMR blogs
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04-15-2011 01:40 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.
nmrlearner
News from NMR blogs
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04-09-2011 12:17 AM
[Question from NMRWiki Q&A forum] NutsPro software to extract a plot from a stacked plot file
NutsPro software to extract a plot from a stacked plot file
Hello,
I was using VnmrJ to collect an array of 6 NMR spectra. I used VnmrJ to save all 6 spectra in 1 fid file by using the svf('filename') command. When opening the fid file in NutsPro to analyze the data, I am able to see all 6 spectra in Stacked Plots mode. They show up as Fid spectra, stacked on top of each other. However I am only able to individually display the first plot and only able to take the Fourier Transform of that first plot in the series. I am unable to select any other plot in that array. Is there a way in...
nmrlearner
News from other NMR forums
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03-04-2011 02:12 AM
[NMR Sparky Yahoo group] add scale along Y axis in the strip plot window
add scale along Y axis in the strip plot window
right now I have to use the aligned 3D dataset to guess the chemical shifts along the Y axis, which is quite inconvenient. I hope there is an easy solution to
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nmrlearner
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08-21-2010 03:03 PM
Got bad PROCHECK Ramachandran plot? Try MolProbity
Don't get good numbers of Ramachandran plot for your protein when you use PROCHEK-NMR? This could be because PROCHEK most favored regions of Ramachandran plot are too small, not because your model is bad. Try to check your protein using MolProbity server from Richardson's lab.
Making Ramachandran plot ?II
Linear Mode
