When I installed PyMol on my iMac using Fink, I found there are some plugins installed already. One of the famous plugin is PDB loader, I believe every one loves it a lot. A new one (at least it’s new to me) is NMR extension written by a Canadian group. Thank you! I’m lovin it [...]
[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
NMR spectroscopy of 14-3-3? reveals a flexible C-terminal extension. Differentiation of the chaperone and phosphoserine binding activities of 14-3-3?
NMR spectroscopy of 14-3-3? reveals a flexible C-terminal extension. Differentiation of the chaperone and phosphoserine binding activities of 14-3-3?
NMR spectroscopy of 14-3-3? reveals a flexible C-terminal extension. Differentiation of the chaperone and phosphoserine binding activities of 14-3-3?
Biochem J. 2011 May 10;
Authors: Williams DM, Ecroyd H, Goodwin KL, Dai H, Fu H, Woodcock JM, Zhang L, Carver JA
Intracellular 14-3-3 proteins bind to many proteins, via a specific phosphoserine motif, regulating diverse cellular tasks including cell...
nmrlearner
Journal club
0
05-12-2011 03:40 PM
ncIDP-assign: A SPARKY extension for the effective NMR assignment of intrinsically disordered proteins.
ncIDP-assign: A SPARKY extension for the effective NMR assignment of intrinsically disordered proteins.
ncIDP-assign: A SPARKY extension for the effective NMR assignment of intrinsically disordered proteins.
Bioinformatics. 2011 Mar 3;
Authors: Tamiola K, Mulder FA
SUMMARY: We describe here the ncIDP-assign extension for the popular NMR assignment programme SPARKY, which aids in the sequence-specific resonance assignment of intrinsically disordered proteins (IDPs). The assignment plugin greatly facilitates the effective matching of a set of...
nmrlearner
Journal club
0
03-05-2011 01:02 PM
Extension of the HA-detection based approach: (HCA)CON(CA)H and (HCA)NCO(CA)H experiments for the main-chain assignment of intrinsically disordered proteins
Extension of the HA-detection based approach: (HCA)CON(CA)H and (HCA)NCO(CA)H experiments for the main-chain assignment of intrinsically disordered proteins
Abstract Extensive resonance overlap exacerbates assignment of intrinsically disordered proteins (IDPs). This issue can be circumvented by utilizing 15N, 13C� and 1HN spins, where the chemical shift dispersion is mainly dictated by the characteristics of consecutive amino acid residues. Especially 15N and 13C� spins offer superior chemical shift dispersion in comparison to 13Cα and 13Cβ spins. However, HN-detected experiments...
nmrlearner
Journal club
0
01-29-2011 05:31 AM
[NMR paper] 1H NMR spectroscopy reveals that mouse Hsp25 has a flexible C-terminal extension of 1
1H NMR spectroscopy reveals that mouse Hsp25 has a flexible C-terminal extension of 18 amino acids.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles 1H NMR spectroscopy reveals that mouse Hsp25 has a flexible C-terminal extension of 18 amino acids.
FEBS Lett. 1995 Aug 7;369(2-3):305-10
Authors: Carver JA, Esposito G, Schwedersky G, Gaestel M
The small heat-shock proteins (Hsps) exist as large aggregates and function by interacting and stabilising non-native proteins in...
S3EPY: a Sparky extension for determination of small scalar couplings from spin-state
Abstract S3EPY is a Python extension to the program Sparky written to facilitate the assessment of coupling constants from in-phase/antiphase and spin-state-selective excitation (S3E) experiments. It enables the routine use of small scalar couplings by automating the coupling evaluation procedure. S3EPY provides an integrated graphical user interface to programs which outputs graphs and the table of determined couplings.
Content Type Journal Article
DOI 10.1007/s10858-009-9392-1
Authors
Petr Novák, Masaryk University National Centre for Biomolecular Research, Faculty of Science...
pynmr ? an excellent PyMol?s NMR extension
Linear Mode
