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11 November 2009

4 November 2009

3 November 2009

30 October 2009

29 October 2009

28 October 2009

26 October 2009

23 October 2009

22 October 2009

21 October 2009

20 October 2009

19 October 2009

15 October 2009

14 October 2009

13 October 2009

12 October 2009

9 October 2009

8 October 2009

  • 15:4815:48, 8 October 2009 diff hist +571‎ N NESG:ProFunc ‎ Created page with '== '''ProFunc''' == [http://www.ebi.ac.uk/thornton-srv/databases/ProFunc/ ProFunc] is a server offered by the [http://www.ebi.ac.uk/Thornton/ Thornton Group] at EBI. It was deve…' current
  • 15:4615:46, 8 October 2009 diff hist +734‎ N NESG:NMRDataArchiving ‎ Created page with '== '''NMR Data Archiving''' == === '''Routine Data Backup''' === Although the Main.HTP server backup data daily, it is required to routinely backup data about project progress. O…'
  • 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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