BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > NMR community > News from other NMR forums
Advanced Search
Home Forums Wiki NMR feeds Downloads Register Today's Posts



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
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:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
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:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
 
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Old 11-08-2012, 09:42 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,732
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default How to create synthetic procpar files for VNMRJ?

How to create synthetic procpar files for VNMRJ?

Hi guys : Im trying to make a procpar for an FID, I know most of the parameters of importance, and have the schema of the procpar in Varian documentation down pretty well. My procpar file imports into common tools such as RNMRTK, NMRPIPE, and iNMR. My problem is that VNMRJ refuses to accept it !

We have noticed that VNMRJ is extremely sensitive to the procpar format. It seems as though VNMRJ really wants to have ALOT (if not ALL) of the procpar parameters that come off of the spectrometer.

This is somewhat surprising to me, since many VNMRJ functions, such as basic processing, only need to know the sweep width and dimension sizes. That is, to do a zero fill or FT, you don't need to know the room temperature, experiment date, etc...

Does anyone know anything about what data VNMRJ requires to be in a procpar which is loaded ? Programs like NMRPipe, iNMR, etc only need a very limited subset of procpar data (i.e. they can basically load just fine as long as they have np, ni, sw, sw1 array , phase, and a couple of other parameters .....



Check if somebody has answered this question on NMRWiki QA forum
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR Sparky Yahoo group] Re: create Sparky peak list from XEASY xxx.prot and xxx.peaks files
Re: create Sparky peak list from XEASY xxx.prot and xxx.peaks files Should be able to just convert the XEASY peak list to SPARKY using: http://www.cerm.unifi.it/Sparky/extension.html then combine the files as a simple text More...
nmrlearner News from other NMR forums 0 05-16-2011 08:22 AM
[NMR Sparky Yahoo group] Re: create Sparky peak list from XEASY xxx.prot and xxx.peaks files
Re: create Sparky peak list from XEASY xxx.prot and xxx.peaks files Hi Judith, There is a nice script from Dr. Eiso http://nmr2.chem.uu.nl/~eiso/help/index.html and peaks2sparky.awk Best Jinwon More...
nmrlearner News from other NMR forums 0 05-16-2011 08:22 AM
[NMR Sparky Yahoo group] create Sparky peak list from XEASY xxx.prot and xxx.peaks files
create Sparky peak list from XEASY xxx.prot and xxx.peaks files Dear Users, my project is partly assigned with XEASY. I want to go on with SPARKY and would like to use my assigned peak lists from XEASY. I was wondering if More...
nmrlearner News from other NMR forums 0 05-16-2011 08:22 AM
[Question from NMRWiki Q&A forum] Software to create shaped pulse files from mathematical equation?
Software to create shaped pulse files from mathematical equation? I would like to create working shaped pulse files in one step starting from mathematical expressions - one for amplitude, another for phase vs. time. Does anyone know software that can do it? Check if somebody has answered this question on NMRWiki QA forum
nmrlearner News from other NMR forums 0 04-12-2011 01:10 PM
[NMR Sparky Yahoo group] Re: create Sparky peak list from XEASY xxx.prot and xxx.peaks files
Re: create Sparky peak list from XEASY xxx.prot and xxx.peaks files Should be able to just convert the XEASY peak list to SPARKY using: http://www.cerm.unifi.it/Sparky/extension.html then combine the files as a simple text More...
nmrlearner News from other NMR forums 0 03-19-2011 07:01 AM
[NMR Sparky Yahoo group] Re: create Sparky peak list from XEASY xxx.prot and xxx.peaks files
Re: create Sparky peak list from XEASY xxx.prot and xxx.peaks files Hi Judith, There is a nice script from Dr. Eiso http://nmr2.chem.uu.nl/~eiso/help/index.html and peaks2sparky.awk Best Jinwon More...
nmrlearner News from other NMR forums 0 03-18-2011 06:51 PM
[NMR Sparky Yahoo group] create Sparky peak list from XEASY xxx.prot and xxx.peaks files
create Sparky peak list from XEASY xxx.prot and xxx.peaks files Dear Users, my project is partly assigned with XEASY. I want to go on with SPARKY and would like to use my assigned peak lists from XEASY. I was wondering if More...
nmrlearner News from other NMR forums 0 03-18-2011 06:51 PM
[Question from NMRWiki Q&A forum] How to create synthetic FID data in either Bruker, Varian or JEOL?
How to create synthetic FID data in either Bruker, Varian or JEOL? Are there tools that allow to create raw data files in vendor format that contain desired data? For example for the testing purposes one might want to write a specific value at all points. Or perhaps there is some other need to store data in the vendor format - is there software for that?
nmrlearner News from other NMR forums 0 08-22-2010 02:30 AM



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



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2024, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 07:22 AM.


Map