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.
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[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
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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
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05-10-2011 07:07 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 But the ranges used in the Ramachandran plot are a bit out of date.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
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04-20-2011 02:51 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
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03-04-2011 02:12 AM
[Louic Vermeer blog] Compiling Aria2, CNS, procheck and aqua for NMR structure calculation
Compiling Aria2, CNS, procheck and aqua for NMR structure calculation
A quick guide to compiling ARIA 2.2, CNS 1.21, AQUA 3.2 and PROCHECK, under Ubuntu Karmic 9.10 (32-bit) If you use Gentoo linux, you can find aria under sci-chemistry (masked by ~x86). Procheck is in the science overlay (see the layman and overlays documentation). Aqua has to be installed manually at the time of writing this
Read complete story on Louic Vermeer blog
nmrlearner
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10-18-2010 09:17 AM
[NMR paper] AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved
AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR.
Related Articles AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR.
J Biomol NMR. 1996 Dec;8(4):477-86
Authors: Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM
The AQUA and PROCHECK-NMR programs provide a means of validating the geometry and restraint violations of an ensemble of protein structures solved by solution NMR. The outputs include a detailed breakdown of the restraint violations, a...
nmrlearner
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08-22-2010 02:20 PM
[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
[NMR Sparky Yahoo group] Re: add scale along Y axis in the strip plot window
Re: add scale along Y axis in the strip plot window
I knew "vs" shows scales, but the problem is it shows both X & Y axes, while I only need Y axis. As a result, the strip that has the scale doesn't align well
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