BMNRC community perl script to create MARS pseudoresidue table from nmrview xpk file

		BioNMR > NMR community > News from other NMR forums
[BMNRC community] perl script to create MARS pseudoresidue table from nmrview xpk file

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

Flexibility from chemical shifts:

RCI

Interactions from chemical shifts:

HADDOCK

Chemical shifts re-referencing:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

Quality Control Check

NMR spectrum prediction:

FANDAS

MestReS

V-NMR

Flexibility from structure:

Backbone S2

Methyl S2

B-factor

Molecular dynamics:

Gromacs

Amber

Antechamber

Chemical shifts prediction:

From structure:

Shiftx2

Sparta+

Camshift

CH3shift- Methyl

ArShift- Aromatic

ShiftS

Proshift

PPM

CheShift-2- Cα

From sequence:

Shifty

Camcoil

Poulsen_rc_CS

Disordered proteins:

MAXOCC

Format conversion & validation:

CCPN

From NMR-STAR 3.1

Validate NMR-STAR 3.1

NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

Thread Tools

Search this Thread

Rate Thread

Display Modes

09-12-2010, 02:01 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

perl script to create MARS pseudoresidue table from nmrview xpk file

perl script to create MARS pseudoresidue table from nmrview xpk file

Please login to access downloadables

Usage:

creat a hsqc xpk file using nmrview
convert this xpk file to sparky

… Read the rest

Go to BMNRC community to find more info about this topic.

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[Question from NMRWiki Q&A forum] How to pick peaks manually in nmrview? How to pick peaks manually in nmrview? Is there any way to pick peaks manually in nmrview using the red/black cursors? Check if somebody has answered this question on NMRWiki QA forum	nmrlearner	News from other NMR forums	0	01-26-2011 04:21 AM
[Question from NMRWiki Q&A forum] Can you pick peaks manually in nmrview? Can you pick peaks manually in nmrview? Is there any way to pick peaks manually in nmrview using the red/black cursors? Check if somebody has answered this question on NMRWiki QA forum	nmrlearner	News from other NMR forums	0	01-25-2011 04:10 AM
[NMR paper] NvAssign: protein NMR spectral assignment with NMRView. NvAssign: protein NMR spectral assignment with NMRView. Related Articles NvAssign: protein NMR spectral assignment with NMRView. Bioinformatics. 2004 May 1;20(7):1201-3 Authors: Kirby NI, DeRose EF, London RE, Mueller GA MOTIVATION: Nuclear magnetic resonance (NMR) protein studies rely on the accurate assignment of resonances. The general procedure is to (1) pick peaks, (2) cluster data from various experiments or spectra, (3) assign peaks to the sequence and (4) verify the assignments with the spectra. Many algorithms already exist for...	nmrlearner	Journal club	0	11-24-2010 09:25 PM
[NMR Sparky Yahoo group] Re: error reading post script file from sparky Re: error reading post script file from sparky Mehul, I've encountered a similar problem when trying to read Sparky generated PostScript files in Inkscape. Here is the workaround I've used: 1. Use "ps2pdf" More...	nmrlearner	News from other NMR forums	0	10-06-2010 02:23 PM
[NMR Sparky Yahoo group] error reading post script file from sparky error reading post script file from sparky Hi Everyone, *** I am trying to print a post script file from sparky using the 'pt' accelerator followed by the save button. It is making a post script file More...	nmrlearner	News from other NMR forums	0	10-06-2010 02:23 PM
NMRView java redraw problem Hi everyone, I hope someone has an easy solution to this annoying problem. Well here it is. I have the newest NMRView java program installed on a fedora core linux operating system. The program was properly installed, however when I pan in any direction, the crosshairs disappear. Any help is welcomed, Tony	eviltwins	NMR Questions and Answers	0	07-07-2006 11:45 PM
NMRView Installation Woes I am trying to install NMRViewJava on my Fedora Core 5 laptop and was wondering if anyone has had problems with the izpack software. The installer opens and then stalls halfway though the process both in su and normal modes. Thanks for the help in advance.	R2-D2	NMR software	2	07-05-2006 04:20 AM
Mars - automatic backbone assignment of proteins Link to the program Mars - robust automatic backbone assignment of proteins. Jung YS, Zweckstetter M. J Biomol NMR. 2004 Sep;30(1):11-23. Abstract: MARS is a program for robust automatic backbone assignment of 13C/15N labeled proteins. It can be applied independent of the assignment complexity, it does not require tight thresholds for establishing sequential connectivity or detailed adjustment of these thresholds, it can work with a wide variety of NMR experiments and it is robust against missing chemical shift information. In case of a known 3D structure, residual dipolar...	nmrlearner	NMR software	0	03-11-2005 09:05 AM

« Previous Thread | Next Thread »

Posting Rules
You may not post new threads You may not post replies You may not post attachments You may not edit your posts BB code is On Smilies are On [IMG] code is On HTML code is On Trackbacks are Off Pingbacks are Off Refbacks are Off