I somehow recently saw some nice presentation of protein structures prepared by MOLMOL. So I wonder how to make similar colors on the secondary structural elements in PyMOL. The top and bottom figures *are made by PyMOL and MOLMOL, respectively. How I did that? Basically, just make highlight color yellow, turn on discrete cartoon color, [...]
[KPWU blog] [PyMOL] customize spectrum colors
customize spectrum colors
Saw a post at recent Pymol mailing list and found the nice example of “spectrumany” at PymolWiki. Here is the example I created using “spectrumany” to show customized spectral colors of the example protein TBEV envelope protein “PDBV entry: 1SVB”. By using the built-in command “spectrum”, one can color the envelope protein in 2 or http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=786&subd=kpwu&ref=&feed=1
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09-11-2012 03:47 PM
[KPWU blog] [PyMOL] different colors of nucleic acid rings
different colors of nucleic acid rings
The image above can be drew followed by steps in*my earlier post, which shows single color of the nucleotide rings and bonds. I saw a discussion list at PyMol forum today that an user requested a way to display different colors of the nucleotide rings. Below is the example image I tested (using PDB: 2WCC). http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=711&subd=kpwu&ref=&feed=1
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05-24-2012 05:54 PM
[KPWU blog] [PyMOL] assign secondary structural regions
assign secondary structural regions
Sometimes I displayed the cartoon view of a protein in PyMOL as the figures shown below that I don’t really see the helix and strands. It often happens when I merged 10 or 20 structures into a NMR ensemble file. All 20 structures are aligned but the secondary structural regions are not clearly displayed http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=559&subd=kpwu&ref=&feed=1
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10-06-2011 09:11 PM
[NMR paper] An NMR view of the unfolding process of rusticyanin: Structural elements that maintain the architecture of a beta-barrel metalloprotein.
An NMR view of the unfolding process of rusticyanin: Structural elements that maintain the architecture of a beta-barrel metalloprotein.
Related Articles An NMR view of the unfolding process of rusticyanin: Structural elements that maintain the architecture of a beta-barrel metalloprotein.
Protein Sci. 2005 Jul;14(7):1710-22
Authors: Alcaraz LA, Jiménez B, Moratal JM, Donaire A
The unfolding process of the blue copper protein rusticyanin (Rc) as well as its dynamic and D(2)O/H(2)O exchange properties in an incipient unfolded state have been...
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12-01-2010 06:56 PM
[NMR paper] Secondary structural effects on protein NMR chemical shifts.
Secondary structural effects on protein NMR chemical shifts.
Related Articles Secondary structural effects on protein NMR chemical shifts.
J Biomol NMR. 2004 Nov;30(3):233-44
Authors: Wang Y
For an amino acid in protein, its chemical shift, delta(phi, psi)(s), is expressed as a function of its backbone torsion angles (phi and psi) and secondary state (s): delta(phi, psi)(s=deltaphi, psi)_coil+Deltadelta(phi, psi)_s), where delta(phi, psi)(coil) represents its chemical shift at coil state (s=coil); Delta delta(phi, psi)(s) (s=sheet or helix) is...
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11-24-2010 10:03 PM
[NMR paper] Sequential assignments and identification of secondary structure elements of the coli
Sequential assignments and identification of secondary structure elements of the colicin E9 immunity protein in solution by homonuclear and heteronuclear NMR.
Related Articles Sequential assignments and identification of secondary structure elements of the colicin E9 immunity protein in solution by homonuclear and heteronuclear NMR.
Biochemistry. 1994 Oct 18;33(41):12347-55
Authors: Osborne MJ, Lian LY, Wallis R, Reilly A, James R, Kleanthous C, Moore GR
1H-1H, 1H-15N, and 1H-1H-15N multidimensional NMR spectroscopic studies of the 86 amino...
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08-22-2010 03:29 AM
[NMR paper] 1H NMR sequential assignments and identification of secondary structural elements in
1H NMR sequential assignments and identification of secondary structural elements in oxidized putidaredoxin, an electron-transfer protein from Pseudomonas.
Related Articles 1H NMR sequential assignments and identification of secondary structural elements in oxidized putidaredoxin, an electron-transfer protein from Pseudomonas.
Biochemistry. 1992 Feb 25;31(7):1961-8
Authors: Ye XM, Pochapsky TC, Pochapsky SS
Sequential 1H resonance assignments and secondary structural features of putidaredoxin (Pdx), a 106-residue globular protein consisting of...
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08-21-2010 11:41 PM
[NMR paper] Determination of the secondary structural elements of chicken liver fatty acid bindin
Determination of the secondary structural elements of chicken liver fatty acid binding protein by two-dimensional homonuclear NMR.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_120x27.gif Related Articles Determination of the secondary structural elements of chicken liver fatty acid binding protein by two-dimensional homonuclear NMR.
Biopolymers. 1999 Jul;50(1):1-11
Authors: Schievano E, Mammi S, Peggion E
A conformational study in solution of the fatty acid...
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[PyMOL] molmol-like colors on secondary structural elements
Linear Mode
