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8 October 2009

  • 15:4515:45, 8 October 2009 diff hist +1,547‎ N NESG:PeakDetectionYield ‎ Created page with '== '''Determination of Peak Detection Yield''' == It is required to determine the peak detection yield of a NMR spectrum as earlier as possible. Determination of approximate pea…'
  • 15:4415:44, 8 October 2009 diff hist +2,030‎ N NESG:FormatConversion ‎ Created page with '== '''NMR Spectra Format Conversion''' == === '''Conversion from Buffalo.NMRPipe Format to XEASY Format''' === After optimizing phase, macro <tt>doit.com</tt> is used to run lin…' current
  • 15:4315:43, 8 October 2009 diff hist +3,136‎ N NESG:AGNuS ‎ Created page with '==*Autoproc/AGNuS* == [http://www-nmr.cabm.rutgers.edu/software/autoproc.htm Autoproc/AGNuS] is a suite of programs for the automatic generation of scripts for multidimensional p…' current
  • 15:4115:41, 8 October 2009 diff hist +11,024‎ N NESG:BuffaloNMRPipeFT ‎ Created page with '== '''Data Processing Protocol''' == In the <tt>process</tt> directory, go to the directory of the experiment you would like to process and check the README file for instru…' current
  • 15:4015:40, 8 October 2009 diff hist +1,660‎ N NESG:TransferDataFromNMRSpectrometer ‎ Created page with '== '''Transfer Data From NMR Spectrometer''' == Go to the <tt>acq</tt> directory under the target directory. Check README for instructions: * This directory will contain ONLY yo…' current
  • 15:3915:39, 8 October 2009 diff hist +1,211‎ N NESG:AutomaticGenerationOfProjectDirectoryTree ‎ Created page with '== '''Automatic Generation of Project Directory Tree''' == A set of multi-dimensional heteronuclear GFT NMR experiments (see [http://pubs.acs.org/cgi-bin/searchRedirect.cgi/jacs…' current
  • 15:3815:38, 8 October 2009 diff hist +544‎ N NESG:BuffaloProcessProctocol ‎ Created page with '== '''Buffalo's Process Proctocol''' == The current Buffalo processing protocols described here have been developed for NMRpipe with help of Perl Scrips developed by Dr. David P…' current
  • 15:3715:37, 8 October 2009 diff hist +835‎ N NESG:DataProcessing ‎ Created page with '== '''Data Processing Overview''' == The current data processing protocols (by using Buffalo scripts or AGNuS) described here are similar as both protocols were designed around …' current
  • 15:3515:35, 8 October 2009 diff hist +3,695‎ N NESG:ExperimentSpecificNMRParameters ‎ Created page with '== '''Experiment-specific NMR Parameters''' == It would be very helpful to start with previously optimized parameter set. * Parameters for 2D Experiments for proteins ** 2D 15N…' current
  • 15:3415:34, 8 October 2009 diff hist +1,043‎ N NESG:OtherNMRParametersOptimization ‎ Created page with '== Other Parameters == === Amplifier Compression === NMR amplifiers normally exhibit non-linear response at the peak power used for high pulses. This non-linearity has to be ta…' current
  • 15:3315:33, 8 October 2009 diff hist +8,840‎ N NESG:SettingUpMultidimensionalNMRExperiments ‎ Created page with '= '''Setting Up Multidimensional NMR Experiments''' = It is recommended to collect different NMR data sets depending on the behavior of the protein, and collect the NOESY spectr…' current
  • 15:3115:31, 8 October 2009 diff hist +1,387‎ N Long-range 15N-1H correlation experiments for histidine rings ‎ Created page with '== 2D [15N, 1H] long-range HSQC for His rings == === Varian === This pulse sequence correlates aromatic H-C protons of His with ring nitrogens. Use the <tt>rna_WGgNhsqclr</tt>…'
  • 15:3015:30, 8 October 2009 diff hist +628‎ N NESG:HCCHTocsY ‎ Created page with '== Aliphatic 3D (H)CCH-TOCSY == Slightly modified version of the <tt>cch_tocsyA.c</tt> in BioPack. * Corrected small uncompensated initial evolution in 13C t1 dimension * Chang…' current
  • 15:2915:29, 8 October 2009 diff hist +1,893‎ N NESG:43DGFTHCCHCosYali ‎ Created page with '== (4,3)D GFT HCCH-COSY Aliphatic == Written by Youlin Xia and H. Atreya. Modified by Main.AlexEletski Requires pre-installed BioPack. [[NESG:%PUBURLPATH%/Buffalo/43DGFTHCCHCo…' current
  • 15:2615:26, 8 October 2009 diff hist +2,145‎ N NESG:43DGFTHabCabconhn ‎ Created page with '== (4,3)D GFT HABCAB(CO)NHN == Written by Youlin Xia and H. Atreya. Modified by Main.AlexEletski Requires pre-installed BioPack. [[NESG:%PUBURLPATH%/Buffalo/43DGFTHabCabconhn/…' current
  • 15:2415:24, 8 October 2009 diff hist +2,208‎ N NESG:43DGFTCabCaconhn ‎ Created page with '== (4,3)D GFT CABCA(CO)NHN == Written by Youlin Xia and H. Atreya. Modified by Main.AlexEletski Requires pre-installed BioPack. [[NESG:%PUBURLPATH%/Buffalo/43DGFTCabCaconhn/g…' current
  • 15:2215:22, 8 October 2009 diff hist +498‎ N 2D (13C, 1H) HSQC for fractionally 13C-labeled samples ‎ Created page with '== 2D [13C, 1H] ct-HSQC for 5% 13C-labeled samples == === Varian === gChsqc_methyl macro will setup a 2D [13C, 1H] constant-time HSQC optimiz…'
  • 15:2115:21, 8 October 2009 diff hist +456‎ N NESG:BuffaloNMRExperimentSet3D ‎ Created page with '=== 3D Experiment Set (Buffalo) === <tt>HTP_3D_Setup</tt> creates the following ready-to-run experiments: * 3D HNCO * 3D CBCA(CO)NH * 3D HNCACB * 3D HBHA(CBCACO)NH * 3D aliphat…' current
  • 15:2015:20, 8 October 2009 diff hist +276‎ N NESG:BuffaloNMRExperimentSetGFT ‎ Created page with '== '''GFT NMR Experiment Set (Buffalo)''' == * 3D HNCO or (3,2)D HNNCO * (4,3)D CABCA(CO)NHN * (4,3)D HNNCABCA * (4,3)D HABCAB(CO)NHN * (4,3)D aliphatic HCCH-COSY * 3D aliphati…' current
  • 15:1915:19, 8 October 2009 diff hist +3,481‎ N Simultaneous 13C,15N-resolved NOESY ‎ Created page with '== Simultaneous 15N-, 13C(ali)-, 13C(aro)-resolved [1H,1H] NOESY == Modified from BioPack <tt>gnoesyCNhsqc.c</tt> by Main.AlexEletski, similar to the previous <tt>cnnoesy.c</tt>…'
  • 15:1715:17, 8 October 2009 diff hist +345‎ N NESG:2DHSQCExperimentSet ‎ Created page with '== 2D HSQC Experiment set == Run <tt>HTP_HSQC_setup</tt> to configure the following 2D experiments: * [15N, 1H]-HSQC * [15N, 1H]-HSQC wide 15N spectral width - to see Arg and H…' current
  • 15:1515:15, 8 October 2009 diff hist +9,815‎ N Measuring 15N T1 and T2 relaxation times (Varian) ‎ Created page with '== '''Correlation Time and NMR Measurement Time Prediction''' == === '''Experimental Setup''' === Run the <tt>HTP_t1t2_setup</tt> script to setup the following experiments: * 2…'
  • 15:1415:14, 8 October 2009 diff hist +860‎ N NESG:First1DAnd2DHSQC ‎ Created page with 'Proton 1D spectrum: # Load the <tt>water</tt> dataset. # Set a large <tt>sw</tt> - you should at least see the range between 15 and -3 ppm for a new protein. Adjust <tt>np</tt> o…' current
  • 15:1215:12, 8 October 2009 diff hist +2,131‎ N NESG:CustomHTPSetupScripts ‎ Created page with '== '''Custom NMR Experiment Setup Scripts for VNMRJ''' == <tt>HTP_t1t2_setup</tt>, <tt>HTP_hsqc_setup</tt> and <tt>HTP_3D_setup</tt> configure several workspaces with ready-to-…' current
  • 15:1115:11, 8 October 2009 diff hist +9,467‎ N NESG:Non-UniformSamplingAndMDD ‎ Created page with '=== Introduction === This section describes the acquisition and processing of non-uniformly sampled 3D data. The intention is to either speed up the acquisition for high sensiti…' current
  • 15:0915:09, 8 October 2009 diff hist +11,274‎ N Deuterium pulse width calibration and decoupling ‎ Created page with '== '''Pulsing and Decoupling on Deuterium Channel''' == The most common application is deuterium decoupling in triple-resonance experiments with deuterated samples. Any time ali…'
  • 15:0515:05, 8 October 2009 diff hist +4,778‎ N Chemical shift referencing ‎ Created page with 'This page describes UIPAC-Recommended referencing procedures. See http://www.bmrb.wisc.edu/ref_info/cshift.html and references therein. Also check the information at the CABM web…'
  • 15:0415:04, 8 October 2009 diff hist +5,445‎ N Temperature calibration ‎ Created page with '== '''Temperature Calibration''' == Temperature control is crucial to NMR experiments. There is always a small discrepancy between the actual temperature of the sample and the t…'
  • 15:0215:02, 8 October 2009 diff hist +3,572‎ N Conditioning procedure for cryogenic probes ‎ Created page with 'The information below is taken from '''Decoupling Noise''' in [http://www.varianinc.com/image/vimage/docs/products/nmr/apps/pubs/manuals/0199919600c.pdf HCN Cold Probe manual] …'
  • 15:0115:01, 8 October 2009 diff hist +729‎ N Rebooting spectrometer console ‎ Created page with '== '''Rebooting of Spectrometers''' == From time to time, NMR spectrometers have been through hardware of software failures which leads to an inactive console. In case of that,…'
  • 15:0015:00, 8 October 2009 diff hist +812‎ N Full probefile calibration ‎ Created page with '== Full Probefile Calibration == This procedure is similar to Automated Pulse Width Calibration, but the number of parameters to be o…'
  • 14:5814:58, 8 October 2009 diff hist +1,246‎ N Installing and updating BioPack ‎ Created page with '== '''Installing And Updating BioPack''' == You have the options of either perfroming a fresh install or an incremental update. Incremental update is quicker, but it requires …'
  • 14:5714:57, 8 October 2009 diff hist +6,346‎ N Pulse width calibration ‎ Created page with '== '''Manual Calibration of Pulse Widths and 1H Carrier Offset''' == === '''Calibration of 1H Carrier Frequency (<tt>tof</tt>)''' === To achieve the best water suppression <tt>…'
  • 14:5614:56, 8 October 2009 diff hist +4,215‎ N NESG:AutomatedNMRParametersOptimization ‎ Created page with '== '''Automated Calibration of 90° pulse widths''' == For every sample you should calibrate 90° pulse widths before acquisition. Here we assume that you have BioPack installe…' current
  • 14:5414:54, 8 October 2009 diff hist +6,322‎ N NESG:BioPackProbefile ‎ Created page with '== BioPack and Probefile == Here we assume that you have BioPack installed. BioPack uses a probefile to store all important parameters for its library of biomolecular NMR pulse …' current
  • 14:5214:52, 8 October 2009 diff hist +12,776‎ N Shimming ‎ Created page with '== '''Sample shimming''' == The shim system is essentially a set of coils with specific field profiles in 3D space. There are three shimming methods: shimming on the lock level,…'
  • 14:5014:50, 8 October 2009 diff hist +7,810‎ N Deuterium Lock ‎ Created page with '== '''Deuterium Lock System''' == The lock system keeps the spectrometer operating at a constant net magnetic field. It compensates for the drift of the superconducting magnet's…'
  • 14:4914:49, 8 October 2009 diff hist +6,114‎ N Tuning and matching ‎ Created page with '== '''Probe Tuning and Matching''' == NMR probes come in various designs, but the typical triple-resonance HCN probe has two coils and four resonant circuits. The inner observe …'
  • 14:4714:47, 8 October 2009 diff hist −266‎ Inserting NMR Sample ‎No edit summary
  • 14:4714:47, 8 October 2009 diff hist +2,411‎ N Inserting NMR Sample ‎ Created page with '== '''Sample Loading''' ==<br><br>=== '''Using the sample gauge''' ===<br><br>The optimal volume for NMR samples is 500-600 uL for 5 mm regular NMR tubes and ~300 uL for Shigemi …'
  • 14:4514:45, 8 October 2009 diff hist +9,921‎ N NMR Sample Preparation ‎ Created page with '== '''Sample Transfer into NMR Tubes''' == Although our lab seldom produces NMR samples we frequently have to transfer the samples to an NMR tube. According to different requir…'
  • 14:3714:37, 8 October 2009 diff hist +5,254‎ N Mass Spectrometry ‎ Created page with '== Compare Mass Spectrometry m/z with Calculated Protein Mass == === Mass Spectrometry Results from SPINE === <br />The mass spectrum chromatogram for many of the purified samp…'
  • 14:3514:35, 8 October 2009 diff hist +3,388‎ N NESG:OligomerizationStatus ‎ Created page with '== '''Assessment of Oligomerization Status''' == === '''Gel-filtration Results from SPINE''' === The oligomerization status of each target is noted in SPINE: * Go to the Batch …'
  • 14:3314:33, 8 October 2009 diff hist −95‎ NESG:SampleCheck ‎No edit summary
  • 14:3314:33, 8 October 2009 diff hist +1,636‎ N NESG:SampleCheck ‎ Created page with '== '''Sample Check''' ==<br><br>=== '''Visual inspection of the sample''' ===<br><br>Once a sample arrives, <br>* Do visual inspection of the sample checking for cloudiness or vi…'
  • 14:3014:30, 8 October 2009 diff hist +5,149‎ N NESG:Acquiring an NMR Sample ‎ Created page with '== '''Acquiring an NMR Sample''' == === '''[http://www.nesg.org NESG] Ordering Procedure''' === One should contact the [http://www.nesg.org NESG] protein production centers for…'
  • 14:2614:26, 8 October 2009 diff hist −5,970‎ NESG:MasterRecipe ‎No edit summary

7 October 2009

6 October 2009

5 October 2009

2 October 2009

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