Introduction to Unix and VNMR
Contents
1. reads parameters save shim settings to user directory vnmrsys shims FILE SAVESHIM reads shims follow with loadshims macro UWMACROS LOADSHIMS saves data to filename at completion of experiment V required for quotes within the main quotes requires au used to start acquisition lists all experiment areas menu MAIN WORKSPACE LIBRARY creates experiment area number see also WORKSPACE deletes experiment area number save disk space see also WORKSPACE UW macro to set temp to 24 C cp into your vnmrsys maclib rename and edit for other temperatures UWMACROS SET TEMP variable temp controller not present 0 or present 2 no temp specificied for control command preceeding probe change see macro tempoff command to re establish temp control at 24 C after probe change see macro temp24 set transmitter to Si frequency uses look up table see macro tuneh set delay time in seconds use dps to make sure about timing common pulse width in usec use dps pulse width in usec use dps observe transmitter power set in dB from 0 to 63 larger is more power observe transmitter fine power control from 0 to 4095 3db spread first set cursor close to peak then finds nearest line first use nl to set cursor exactly on then sets reference expand about correct reference on diagonal peak use to ref f7 axis gives exponential broadening of 5 hertz with wft or ga UWChem MR Varian NMR User s Guide2. shims move to home account for computer working at export home username moves to export home fry on vorlon workstation reads data fid file datafile name must have fid as suffix vnmr always appends as such with svf command all datafile fid files are actually directories containing IG shine ease ai aaa a aed actual fid data NG Bese neh Acces Ae oe hu A log file shows times for acquisitions PLOCP ar sess ches eee eset eet processing parameters COX Ge sordevs heeevesteseetied Geaeesest a text file created by command text reads parameter file parfile name must have par as suffix vnmr always appends as such with svp command all parfile par files have only procpar and text files data acquisition area can go up to exp9 but can take significant disk space user macro library user manual help for pulse sequences directory user menu definitions directory user created or modified pulse sequences user compiled pulse sequences user created RF and gradient shapes e g for NOES Y1D user stored shim files system macro library system manual help for pulse sequences directory system menu definitions directory system pulse sequences system compiled pulse sequences system stored RF and gradient shapes e g for NOES Y1D system facility stored shim files IV Common Pulse Sequence Setup in VNMR this section is directed at students wanting to know details of the vnmr psg setups 1 Always start by r
3. wit aph np 4k fn 16k Isfid 2 movesw CZ be be 5 pl text text goes here atext more text pap ppa axis p pscale 3 axish pscale 6 page clradd spadd addi s1 ri md 3 4 dssh full dss Page 12 weighted depending on parameters set FT good automatic phase to at least start phasing often set by sw this directly sets to 4096 points acquired changes aq number FT to with previous command does two zero fills left shift two points before FT increase if getting baseline rolling macro sets sweep width sw to right and left cursor positions zero all integral resets use menu button reset and mouse for resets baseline correction with default spline fit depends on integral resets baseline correction using 5th order polynomial fit plot spectra um as displayed text header plotted on top of page adds lines to text header plot all parameters plot only a few parameters set axis to ppm h for hertz k for kilohertz plot scale in current units macro to set Hz scale and plot axis 6 cm below spectrum go to next page for plotting clear exp5 and place current spectrum in exp5 setup for addi add sub dual display like routine save display parameters can use s1 through s9 recall display 1 and display as previously saved with s1 move saved display regions s1 to s9 from exp3 to exp4 display stack horizontally return display of one spectrum to full width display stack using
4. v0 and h0 as vertical and horizontal offsets UWChem2 R macros tuneh tunesi tunec loadshims axisp axish dsx invert tempoff tn H1 gain O SU en S use UWMACROS TUNE H1 tn Si29 gain O SU eee ceeeeeeteceeneceeeeees use UWMACROS TUNE S129 tn C13 gain 0 su load y su load N uu ce eeeeeececeseceesteeeeeeeeeeeees UWMACROS LOADSHIMS axis p axis h wit dscale 3 rp rp 180 inverts the 0 order phase of a spectrum vttype 0 temp N SU oo eee crucial command before probe change UWCheM HRI Quick Guide for New Users Page 13 temp24 vitype 2 temp 24 su vttype O SU model temp macro settemp vttype 2 temp x su wait vttype 0 su intnorm normalizes peak to user specified value e g methyl peak to 3 disp2d sets up wp sc nicely for 2d plots pconpos plots contours of 2D spectra with positive peaks getting 10 contours negative peaks getting just 1 pconneg opposite of pconpos Ipforward sets up for forward linear prediction UWCheM HRI Intro to Unix and VNMR Page 14 lll VNMR Directory Structure There is a user vnmrsys area and a system vnmr area All files are looked for in user area first if not found there then the system area is checked cd cd vorlon fry rtf datafile rtp parfile vnmrsys exp1 maclib manual menulib psglib seqlib shapelib shims vnmr maclib manual menulib psglib seqlib shapelib
5. Varian VNMR User s Guide Page 10 Introduction to Unix and VNMR created 3 5 95 updated 12 19 01 Il Common Unix Commands cd change directory to home dir you first go to on login cd vnmrsys change to your vnmr directory pwd show current location path df k display file system will show free space amp paths see section III on directory structures mkdir make directory rmdir remove directory man cmnd show manual pages for cmnd Is list files Is la list files with options lga alias dir Is la in your cshre file cp r name copy recursively from name down path i e including all subdirectories mv fname tname move fname to tname i e a rename unless a change in path is specified rm r name remove from name down path including all subdirectories use care this is a dangerous command Use the text editor in the CDE windowed environment if possible much easier than vi but always finish with a carriage return at the end of the file when creating macros In addition you can use fextedit filename ata unix prompt to bring up the more usable textedit editor vi filename edit filename using vi editor cgfhas couple pages of Vi Quick Reference i insert must use ESC or double up down arrow to exit insert mode a append insert after cursor position use at end of line x delete single character 10x will delete 10 characters dd d
6. b and compiled The compiled code is automatically placed into the user s vnmrsys seqlib which must then be copied into vnmr seqlib and have the owner set to vamrl nmr e g chown vnmril nmr vnmr seqlib relayh root permission is required for the copy and chown unless the user is vnmrl When writing or editing a pulse sequence it is easiest to begin with a premade parameter set New parameters must be created with the create parameter lt type lt tree gt gt command See section 5 2 in the Pulse Programming manual It is important to correct define the parameter when creating it e g when making a new variable dpw2d for a decoupler power setting that should not go above 35 to prevent probe damage use the command create dpw2d integer and follow that with setlimit dpw2d 35 0 1 Note that pulse length parameters should be defined with create pwsl pulse to insure the units for the pulse are in us See the create command information in the vnmr documentation for other parameter types Some newer sequences being written at Varian usually now use a phase table named the same as the sequence and located in vnmr tablib although the newest sequences avoid the use of tablib by specifying the table within the pulse sequence itself rather than externally Typically the macro finishes by setting some parameters directly and then displaying the help file for the sequence that resides in vnmr manual via the command ma
7. eading in standard parameters using MAINMENU SETUP UWChem MR Quick Guide for New Users Page 15 10 Then continue by running a macro e g cosy runs the cosy macro in vnmr maclib or use SETUP SEQUENCE Cosy reads in the same macro The better macros read in only the parameters specified in psgset macro statements within the primary macro routine only ProteinPack macro do not and use rtp instead Typically the parameter file found in vnmr parlib has the same name as the macro but not always e g macro hmqc has statement psgset hmqc13c dg dg1 pwx pwxlvl dpwr which reads the specified parameters in from vnmr parlib hmqc13c Reading in dg and dg1 setup the appearance of the parameter display in the dg and dg1 screens The macros for 2d sequences call another macro set2d that sets up np fn ni fn1 based on the desired digital resolution e g set2d dqcosy 3 6 sets up 3 Hz pt in F2 and 6 Hz pt in F1 Usually but not always set2d sets the actual pulse sequence used e g inside set2d isa statment seqfil 1 where 1 is the first parameter passed into the macro i e in this case the sequence name seqfil is the compiled pulse sequence psg residing in vnmr seqlib The pulse sequence source C code resides in vnmr psglib The source code is compiled with the statement seqgen e g for cosy seqgen relayh c Only users and vnmr1 can compile source code so common code must be placed in the user s vnmrsys psgli
8. elete single line A move to beginning of line then use i to insert at beginning of line move to end of line then use a to insert at end of line wq write and end vi session q quit discard changes text lt ret gt go to next occurrance of text set number gives line numbers help with debugging UWChem MR Intro to Unix and VNMR Page 11 Common VNMR Commands Parameters and Flags particularly useful commands dg dg1 dgs dps da array full wysiwyg n svf filename rtf filename svp filename rtp filename svs filename rts filename wexp svf filename explib cexp delexp temp24 vttype 0 or 2 temp n vttype 0 temp n su vttype 2 temp 24 su tn Si29 d e g dl 1 pw 8 p e g p2 4000 tpwr tpwrf nl rl 9 86p rli 9 86p lb 5 display group normal parameters display second processing plot parameters display shim group display pulse sequence display array powerful array command for stacked acquisition kinetic exps pw checks uses full screen needed after dssh and other commands is NOT the same as the DISPLAY INTERACTIVE FULL button sets display so scaling does NOT match printer save file 1d or 2d with associated data phasing etc FILE SAVEFID reads file menu alternative MAIN MENU FILE save only parameters 1d or 2d significant savings in disk space
9. n relayh as and example for cosy Keep in mind that all vnmr usage looks for macros parameters pulse sequences etc in the userlib vnmrsys first and uses that copy if it exists prior to looking in the system area vnmr Thus every user can have their own version not recommended of the same sequence User s are encouraged to copy a sequence into a new name in their own directory Finally I am beginning to implement an intermediate area for facility developed software e g maclibpath vnmr maclib path VNMR will look first at vnmrsys then at vnmr maclib path and last vnmr for a macro I will update documentation here when this implmentation is done UWCheM HRI
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