NESG Wiki - User contributions [en]

Spectra Format Conversion from NMRPipe Data

2023-01-26T20:11:50Z

Suryaven:

'''Spectra Format Conversion from NMRPipe Processed Data'''

 

===== NMRPipe to Sparky =====

:Type the following command in the UNIX terminal
::For a 2D dataset 'gnhsqc.ft2' ([https://nesgwiki.chem.buffalo.edu/index.php/Routine_2D_Experiment])

:::pipe2ucsf gnhsqc.ft2 gnhsqc.ucsf
::For a 3D dataset ([https://nesgwiki.chem.buffalo.edu/index.php/Routine_Processing_Procedure_for_3D_15N_and_13C-edited_Experiments Routine Processing Procedure for 3D 15N and 13C-edited Experiments])

:::Use xyz2pipe to combine 2D planes into one single PIPE file (Go to the directory where the 3D planes are stored)

::::xyz2pipe -in test%03d.ft3 -x > 3D_HNCO.mat

:::Convert the single PIPE file to UCSF format

::::pipe2ucsf 3D_HNCO.mat 3D_HNCO.ucsf

:Additional information can be found in [http://www.cgl.ucsf.edu/home/sparky/manual/index.html Sparky Manual] <ref>T. D. Goddard and D. G. Kneller, SPARKY 3, University of California, San Francisco </ref>

===== NMRPipe to CARA =====

===== NMRPipe to XEASY =====

===== NMRPipe to NMRViewJ =====

:At the end of the processing script (e.g. ft2d.com or nmrproc.com), insert the following two lines:
::For 2D dataset ([https://nesgwiki.chem.buffalo.edu/index.php/Routine_2D_Experiment Routine Processing Procedure for 2D Experiment])
:::
:::nmrPipe -in gnhsqc.ft2 \
:::|pipe2xyz -nv -out filename.nv

::For a 3D dataset ([https://nesgwiki.chem.buffalo.edu/index.php/Routine_Processing_Procedure_for_3D_15N_and_13C-edited_Experiments Routine Processing Procedure for 3D 15N and 13C-edited Experiments])
:::
:::xyz2pipe -in lp/test%03d.ft3 -x \
:::|pipe2xyz -nv -out filename.nv

===== References =====

<references /> Updated by Hsiau-Wei Lee, 2011

Spectra Format Conversion from NMRPipe Data

2023-01-26T20:09:37Z

Suryaven:

'''Spectra Format Conversion from NMRPipe Processed Data'''

 

===== NMRPipe to Sparky =====

:Type the following command in the UNIX terminal
::For a 2D dataset 'gnhsqc.ft2' ([https://nesgwiki.chem.buffalo.edu/index.php/Routine_2D_Experiment])

:::pipe2ucsf gnhsqc.ft2 gnhsqc.ucsf
::For a 3D dataset ([https://nesgwiki.chem.buffalo.edu/wiki/Routine_Processing_Procedure_for_3D_15N_and_13C-edited_Experiments Routine Processing Procedure for 3D 15N and 13C-edited Experiments])

:::Use xyz2pipe to combine 2D planes into one single PIPE file (Go to the directory where the 3D planes are stored)

::::xyz2pipe -in test%03d.ft3 -x > 3D_HNCO.mat

:::Convert the single PIPE file to UCSF format

::::pipe2ucsf 3D_HNCO.mat 3D_HNCO.ucsf

:Additional information can be found in [http://www.cgl.ucsf.edu/home/sparky/manual/index.html Sparky Manual] <ref>T. D. Goddard and D. G. Kneller, SPARKY 3, University of California, San Francisco </ref>

===== NMRPipe to CARA =====

===== NMRPipe to XEASY =====

===== NMRPipe to NMRViewJ =====

:At the end of the processing script (e.g. ft2d.com or nmrproc.com), insert the following two lines:
::For 2D dataset ([https://nesgwiki.chem.buffalo.edu/wiki/Routine_2D_Experiment Routine Processing Procedure for 2D Experiment])
:::
:::nmrPipe -in gnhsqc.ft2 \
:::|pipe2xyz -nv -out filename.nv

::For a 3D dataset ([https://nesgwiki.chem.buffalo.edu/wiki/Routine_Processing_Procedure_for_3D_15N_and_13C-edited_Experiments Routine Processing Procedure for 3D 15N and 13C-edited Experiments])
:::
:::xyz2pipe -in lp/test%03d.ft3 -x \
:::|pipe2xyz -nv -out filename.nv

===== References =====

<references /> Updated by Hsiau-Wei Lee, 2011

Spectra Format Conversion from NMRPipe Data

2023-01-26T02:09:08Z

Suryaven:

'''Spectra Format Conversion from NMRPipe Processed Data'''

 

===== NMRPipe to Sparky =====

:Type the following command in the UNIX terminal
::For a 2D dataset 'gnhsqc.ft2' ([http://www.nmr2.buffalo.edu/wiki/Routine_2D_Experiment Routine Processing Procedure for 2D Experiment])

:::pipe2ucsf gnhsqc.ft2 gnhsqc.ucsf
::For a 3D dataset ([https://nesgwiki.chem.buffalo.edu/wiki/Routine_Processing_Procedure_for_3D_15N_and_13C-edited_Experiments Routine Processing Procedure for 3D 15N and 13C-edited Experiments])

:::Use xyz2pipe to combine 2D planes into one single PIPE file (Go to the directory where the 3D planes are stored)

::::xyz2pipe -in test%03d.ft3 -x > 3D_HNCO.mat

:::Convert the single PIPE file to UCSF format

::::pipe2ucsf 3D_HNCO.mat 3D_HNCO.ucsf

:Additional information can be found in [http://www.cgl.ucsf.edu/home/sparky/manual/index.html Sparky Manual] <ref>T. D. Goddard and D. G. Kneller, SPARKY 3, University of California, San Francisco </ref>

===== NMRPipe to CARA =====

===== NMRPipe to XEASY =====

===== NMRPipe to NMRViewJ =====

:At the end of the processing script (e.g. ft2d.com or nmrproc.com), insert the following two lines:
::For 2D dataset ([https://nesgwiki.chem.buffalo.edu/wiki/Routine_2D_Experiment Routine Processing Procedure for 2D Experiment])
:::
:::nmrPipe -in gnhsqc.ft2 \
:::|pipe2xyz -nv -out filename.nv

::For a 3D dataset ([https://nesgwiki.chem.buffalo.edu/wiki/Routine_Processing_Procedure_for_3D_15N_and_13C-edited_Experiments Routine Processing Procedure for 3D 15N and 13C-edited Experiments])
:::
:::xyz2pipe -in lp/test%03d.ft3 -x \
:::|pipe2xyz -nv -out filename.nv

===== References =====

<references /> Updated by Hsiau-Wei Lee, 2011

Main Page

2022-11-29T02:29:40Z

Suryaven: /* nmr 2.0 */

__NOTOC__

<big>'''Welcome to the NESG Wiki!'''</big> 

The NESG Wiki is a medium for sharing experimental protocols as well as training an educational materials in the fields of structural biology, structural genomics and biomolecular NMR.

Please check out [[NESG NMR wiki workshop at the 2010 Keystone meeting|NESG NMR wiki workshop presentations at the 2010 Keystone meeting]]

== Protein Sample Production ==

{| cellspacing="1" class="FCK__ShowTableBorders"
|- valign="top"
|
*[[Target selection|NESG target selection]] 
*[[DNA cloning protocols|DNA cloning protocols]] 
*[[Protein purification|Protein expression and purification protocols]]  
*Sample Optimization
**[[Construct optimization]]
**[[Buffer optimization]]
**[[Cofactor optimization]]

|
*Protein Sample Analysis
**[[SDS page gel]]
**[[Protein concentration|Protein concentration measurements]]
**[[Oligomerization Status|Assessment of Oligomerization State]]
***[[Gel filtration and light scattering|gel-filtration and light scattering]]
***[[NMR determined Rotational correlation time]]
**[[MassSpectrometry|Mass spectrum]]
**[[NMR screening]]

|}

== NMR Data Acquisition ==

{| class="FCK__ShowTableBorders" cellspacing="1"
|- valign="top"
|
*Routine operation
**[[NMR Sample Preparation]]
**[[Inserting NMR Sample]]
**[[Tuning and matching]]
**[[Deuterium Lock]]
**[[Shimming]]
**[[Pulse width calibration]]
**[[Temperature calibration]]
**[[Chemical shift referencing]]
*Advanced operation
**[[Deuterium pulse width calibration and decoupling]]

|
*NMR data acquisition for protein structure determination
**[[Common NMR experiment sets]]
**[[NMR experiment setup scripts for VNMRJ|Custom NMR experiment setup scripts for VNMRJ]]
**[[Estimation of rotational correlation time]]
**[[Estimation of measurement time]]
**[[Simultaneous 13C,15N-resolved NOESY]]
**[[2D (13C, 1H) HSQC for fractionally 13C-labeled samples|2D [13C, 1H]-HSQC for fractionally 13C-labeled samples]]
**[[Long-range 15N-1H correlation experiments for histidine rings]]
*[[Setting up non-uniformly sampled spectra|Non-uniform sampling (NUS) ]]
**[[Setting up non-uniformly sampled spectra/NUS guide for Varian|NUS - Varian]]
**[[Setting up non-uniformly sampled spectra/NUS guide for Bruker according to Arrowsmith group in Toronto|NUS - Bruker]]

|
*Maintenance (VARIAN)
**[[Installing and updating BioPack]]
**[[Full probefile calibration]]
**[[Rebooting spectrometer console]]
**[[Conditioning procedure for cryogenic probes]]

|}

== NMR Data Processing ==

{| class="FCK__ShowTableBorders" cellspacing="1"
|- valign="top"
|
NMRPipe

*[[Brief description of philosophy, commands, and functions of NMRPipe|Brief description of philosophy, commands, and functions]]
*[[Routine 2D Experiment|2D experiments]]
*[[Routine Processing Procedure for 3D 15N and 13C-edited Experiments|3D 15N and 13C-edited experiments]]
*[[HSQCTROSY RDC Measurement|2D ]][[HSQCTROSY RDC Measurement|15]][[HSQCTROSY RDC Measurement|N HSQC-TROSY experiment for RDC measurement]]
*[[Jmodulation Experiment RDC|2D J-modulation experiment for RDC measurement]]
*[[Alignment Media Preparation|Alignment Media Preparation for RDC measurement]]

|
Other

*[[Processing NMR spectra with PROSA|PROSA]]
*[[Bruker Data Processing|TOPSPIN]]
*[[AGNuS/AutoProc|AUTOPROC]]
*[[Processing non-uniformly sampled spectra with Multidimensional Decomposition|Processing NUS spectra with MDD]]
*[[Spectra Format Conversion from NMRPipe Data|NMRPipe processed data conversion to Sparky, CARA, XEASY, and NMRViewJ]]

|}

== NMR Resonance Assignment ==

*[[Resonance Assignment/Principles and concepts|Principles and concepts]]

{| class="FCK__ShowTableBorders" cellspacing="1"
|- valign="top"
|
*Semi-automated protocols
**[[Resonance Assignment/CARA|CARA]]
**[[Sparky]]
**[[Resonance Assignment/XEASY|XEASY]]

|
*Automated resonance assignment
**[[AutoAssign|AutoAssign]]
**[[AutoAssign WebServer|AutoAssign server]]
**[[Abacus|ABACUS]]
**[[The PINE Server|PINE server]]

|
*Validation and deposition
**[[AVS|Assignment validation suite (AVS)]]
**[[LACS|Linear analysis of chemical shift (LACS)]]
**[[PDB and BMRB Deposition#Preparing_files_for_BMRB_depostion|Depositing chemical shifts]]

|}

== Structure Calculation and Validation ==

[[Structure Calculation and Validation|Principles and concepts]]

{| class="FCK__ShowTableBorders" cellspacing="1"
|- valign="top"
|
*Structure calculation
**[[CYANA Structure Determination Program|CYANA]]
**[[AutoStructure Structure Determination Program|AutoStructure]]
**[[Structure Calculation Using CS-Rosetta|CS-ROSETTA]]
**[[Structure Calculation Using CS-DP ROSETTA|CS-DP ROSETTA]]
**[[Structure Calculation Using CS-RDC-ROSETTA|CS-RDC-ROSETTA]]
**[[Consensus Approaches|"Consensus" approaches]]
**[[Refinement Strategies|Refinement Strategies]]

|
*Special topics
**[[Protein-Ligand Complexes|Protein-Ligand complexes]]
**[[Working With Metal Ions|Metal ions]]
**[[Residual Dipolar Couplings in Structure Refinement|Residual Dipolar Couplings]]
**[[REDCAT|REDCAT]] and [[REDCRAFT|REDCRAFT]]
**[[Paramagnetic Constraints in Structure Determination|Paramagnetic constraints]]
**[[RDC-Assisted Dimer Structure Determination|RDC-assisted dimer structure calculation]]

|
*Structure Refinement
**[[Structure Refinement Using CNS Energy Minimization With Explicit Water|CNS refinement]]
**[[Structure Refinement Using XPLOR-NIH|XPLOR-NIH refinement]]
**[[Rosetta High Resolution Protein Structure Refinement Protocol|ROSETTA refinement]] 

|
*Validation and deposition
**[[PdbStat|PdbStat]]
**[[PSVS|PSVS]]
**[[RPF Analysis|RPF analysis]]
**[[MolProbity Server|MolProbity server]]
**[[RDCvis & KiNG|RDCvis]]
**[[PDB and BMRB Deposition|PDB and BMRB deposition]]
**[[ADIT-NMR|ADIT-NMR]]
**[[HarvestDB|HarvestDB]]
**[[SPINS|SPINS]]

|}