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



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  
Unread 07-25-2011, 11:01 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 22,073
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 adjusting topshim parameters

adjusting topshim parameters

On our Avance III 500 we use Topshim quite successfully for any probe with a gradient coil. The only time we have a problem is with CDCl3 solvent on our 1.7 mm TXI probe, where Topshim fails with a complaint about the signal to noise ratio being too low. This is not surprising for a microprobe, as CDCl3 has the lowest signal of any common deuterated solvent. We have confirmed that the 2H pulse length is correct in the prosol file.

An obvious solution would be to increase the nunber of scans for this probe/solvent combination. There seem to be probe and solvent specific parameter files in the topshim folder (under ..\conf\instr). I have tried making some changes to these files in the obvious places, but the number of scans used always seems to remain at the default (4 for 2H).

Does anyone know how to do this properly?

Thanks

-Kirk



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
[Question from NMRWiki Q&A forum] topshim giving worse lineshape
topshim giving worse lineshape HION bruker av-500 topshim giving worse line shape spectra for e.g it is getting the right keys but in wrong direction I mean it is adding too much in z3 and z5 but manualy it is nedded to minus.have any body any idea why it is?Thanks in advance for answering. with best regardferoon Check if somebody has answered this question on NMRWiki QA forum
nmrlearner News from other NMR forums 0 09-10-2011 08:52 PM
[NMRwiki tweet] nmrwiki: How to adjust topshim parameters? #nmr @bruker http://t.co/9lopPjA
nmrwiki: How to adjust topshim parameters? #nmr @bruker http://t.co/9lopPjA nmrwiki: How to adjust topshim parameters? #nmr @bruker http://t.co/9lopPjA Source: NMRWiki tweets
nmrlearner Twitter NMR 0 07-25-2011 11:10 PM
[Question from NMRWiki Q&A forum] same parameters but difference in phase why?
same parameters but difference in phase why? hi, though this question seems to be easy for you but i am new for this software and to this field. Recently, i took silicon spectra in 500mhz(bruker) seems to be good (i.e.one silicon peak and one nmr tubes broad peak) but when i used same parameters for another sample where i got single peak as i expected but nmr tube peak is inverse this time. I just copied previous parameters only why i got such a inverse signal.If anybody know please help me. thank you Check if somebody has answered this question on NMRWiki QA forum
nmrlearner News from other NMR forums 0 03-31-2011 09:21 PM
[NMR paper] Determination of protein structures consistent with NMR order parameters.
Determination of protein structures consistent with NMR order parameters. Related Articles Determination of protein structures consistent with NMR order parameters. J Am Chem Soc. 2004 Jul 7;126(26):8090-1 Authors: Best RB, Vendruscolo M Order parameters obtained from NMR experiments characterize distributions of bond vector orientations. Their interpretation, however, usually requires the assumption of a particular motional model. We propose a multiple-copy simulation method in which the experimental order parameters are used as restraints in...
nmrlearner Journal club 0 11-24-2010 09:51 PM
[NMR paper] Temperature dependence of NMR order parameters and protein dynamics.
Temperature dependence of NMR order parameters and protein dynamics. Related Articles Temperature dependence of NMR order parameters and protein dynamics. J Am Chem Soc. 2003 Sep 17;125(37):11158-9 Authors: Massi F, Palmer AG The helical subdomain, HP36, of the F-actin-binding headpiece domain of chicken villin, is the smallest naturally occurring polypeptide that folds to a thermostable compact structure. Unconstrained molecular dynamics simulations and constrained molecular dynamics simulations using umbrella sampling are used to study the...
nmrlearner Journal club 0 11-24-2010 09:16 PM
[NMR paper] Changes in the NMR-derived motional parameters of the insulin receptor substrate 1 ph
Changes in the NMR-derived motional parameters of the insulin receptor substrate 1 phosphotyrosine binding domain upon binding to an interleukin 4 receptor phosphopeptide. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Changes in the NMR-derived motional parameters of the insulin receptor substrate 1 phosphotyrosine binding domain upon binding to an interleukin 4 receptor phosphopeptide. Biochemistry. 1997 Apr 8;36(14):4118-24 Authors: Olejniczak ET, Zhou MM, Fesik SW Proteins recognize...
nmrlearner Journal club 0 08-22-2010 03:31 PM
[NMR paper] Changes in the NMR-derived motional parameters of the insulin receptor substrate 1 ph
Changes in the NMR-derived motional parameters of the insulin receptor substrate 1 phosphotyrosine binding domain upon binding to an interleukin 4 receptor phosphopeptide. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Changes in the NMR-derived motional parameters of the insulin receptor substrate 1 phosphotyrosine binding domain upon binding to an interleukin 4 receptor phosphopeptide. Biochemistry. 1997 Apr 8;36(14):4118-24 Authors: Olejniczak ET, Zhou MM, Fesik SW Proteins recognize...
nmrlearner Journal club 0 08-22-2010 03:03 PM
Script to obtain order parameters from a structure
A Python script for prediction of order paramter from a structure is available from this website. The script is based on the following paper F. Zhang and R. Brüschweiler (2002) "Contact Model for the Prediction of NMR N-H Order Parameters in Globular Proteins" J. Am. Chem. Soc. 124(43), 12654-12655.
nmrlearner NMR dynamics 0 05-07-2005 09:21 AM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This 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



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



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2022, 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 08:10 PM.


Map