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

Go Back   BioNMR > Software > NMR software
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 04-13-2007, 05:20 PM
Junior Member
 
Join Date: Apr 2007
Posts: 2
Points: 14, Level: 1
Points: 14, Level: 1 Points: 14, Level: 1 Points: 14, Level: 1
Level up: 27%, 36 Points needed
Level up: 27% Level up: 27% Level up: 27%
Activity: 0%
Activity: 0% Activity: 0% Activity: 0%
NMR Credits: 0
NMR Points: 14
Downloads: 0
Uploads: 0
Default How do I make ambiguous assignments in NMRView for Aria?

Hi,

I'm trying to learn NMRView.

If one has an overlapped peak (multiple possible assignments) and wishes to leave this peak as ambiguous for ARIA to decide on, how does one 'assign it' as ambiguous in NMRView?

I suspect either of the following:

1) Leave question marks in the assignment boxes (aka leave the peak unassigned aka do nothing)

Or

2) Make multiple tentative assignments for the peak (by using the ctrl button in the Peak Identification menu to highlight multiple possibilities, and then pressing 'Assign')

Or

3) Performing step 2) and then putting question marks beside each tentative assignment

Or

4) All of this is irrelavent because Aria automatically treats every peak, in cases where multiple assignments exist, as ambiguous, and then figures out, through iterative calculations, what the best assignments would be

I've read conflicting information on this question. You're advice would be tremendously appreciated.

Thank you for your time,

John
Reply With Quote


Did you find this post helpful? Yes | No

  #2  
Old 04-27-2007, 08:25 PM
Junior Member
 
Join Date: Apr 2007
Posts: 2
Points: 14, Level: 1
Points: 14, Level: 1 Points: 14, Level: 1 Points: 14, Level: 1
Level up: 27%, 36 Points needed
Level up: 27% Level up: 27% Level up: 27%
Activity: 0%
Activity: 0% Activity: 0% Activity: 0%
NMR Credits: 0
NMR Points: 14
Downloads: 0
Uploads: 0
Default

I emailed Bruce Johnson, the software developer, but didn't get a reply.
Reply With Quote


Did you find this post helpful? Yes | No
Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[Question from NMRWiki Q&A forum] Why do unpaired electrons make NMR measurements difficult?
Why do unpaired electrons make NMR measurements difficult? Can someone please answer this for me? Check if somebody has answered this question on NMRWiki QA forum
nmrlearner News from other NMR forums 0 09-19-2011 04:45 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] Automated NOESY interpretation with ambiguous distance restraints: the refined NMR so
Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin. J Mol Biol. 1997 Jun 13;269(3):408-22 Authors: Nilges M, Macias MJ, O'Donoghue SI, Oschkinat H We have used a...
nmrlearner Journal club 0 08-22-2010 03:31 PM
[NMR paper] Automated NOESY interpretation with ambiguous distance restraints: the refined NMR so
Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin. J Mol Biol. 1997 Jun 13;269(3):408-22 Authors: Nilges M, Macias MJ, O'Donoghue SI, Oschkinat H We have used a...
nmrlearner Journal club 0 08-22-2010 03:03 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
How much does a NMR technician usually make?
http://www.chem.unl.edu/nmr/400mhz.htmlwell our professor said it was around 8 k a month, but im just seeing if those figures are correctim guessin no one has any of these at their school?
Bleeble Blabble NMR Questions and Answers 6 10-29-2002 02:02 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 09:40 PM.


Map