#Userlib/maclib This repository contains the userlib/maclib contributions for VnmrJ as packaged in VnmrJ 4.2
##NOTES & CAUTIONS
- Many of these contributions were incorporated into the core VnmrJ software years ago, so may be redundant with core capabilities
- Most of the contributions are obsolete.
- Though many contributions work, there is often a better way of doing things in the more modern software
- These contributions are not guaranteed to work
- These tools may work on some systems but not others. Many will only work with certain versions of VnmrJ, VNMR, RHEL, or Solaris.
- Use these tools at your own risk. Some of them, such as pulse sequences, could potentially damage hardware, and neither Agilent nor UO is responsible for such damage.
- Though this is the User Library, users' contributions are mixed with those from Varian and Agilent staff. On Spinsights, similar Agilent-provided materials like Chempack are available in Toolkit, and shared materials from users/customers are here in User Library. Agilent staff still do contribute to the currently active User Library, but, like all other contributions, those are personal materials that they have developed and find useful, and they are not officially supported by Agilent or guaranteed to work.
- The last update to this file was performed on February 1, 2013, and it will not be updated again.
- This initially should only contain contributions from Agilent and/or Varian but your contributions are welcome
##Downloading You may download this repository from GitHub at: https://github.com/OpenVnmrJ/maclib.git
##Updating and adding
- Fork on GitHub
- Do not add your contribution to the master branch
- If updating contribution, checkout the tag of the contribution, update and commit on the contribution branch
- If adding a new contribution, checkout a new branch with the name of the contribution, push the new branch to your repository, add and commit on the new branch
- Tag your update of change with the name of the contribution, followed by a version, for example, mymacro-v1.1
- Push your branch to your fork; remember to push the tags too
- Make a pull request to the OpenVnmrJ repository
##Contributions
Below is a list of each contribution. To access a contributions, check out its tag
##acq3dpl
acquires 3D spectra as a series of f1f3 planes (no 3D processing with VnmrJ / VNMR, but gives faster access to the first 3D plane).
To install the contribution, checkout the tag acq3dpl-v1.0:
git checkout acq3dpl-v1.0
then read acq3dpl.README
Usually use extract to install the contribution:
extract maclib/acq3dpl
##batchprocess
To install the contribution, checkout the tag batchprocess-v1.0:
git checkout batchprocess-v1.0
then read batchprocess.README
Usually use extract to install the contribution:
extract maclib/batchprocess
##bcdc
"bcdc" uses the "bc" command in a way that prevents flattening broad signals that "region" failed to integrate: "bcdc" does an individual, linear correction on every baseline (= not integrated) region. Useful for automatic integration in automation, especially if samples contain broad signals from exchangeable protons. "bcdc" was written in cooperation with / based on suggestions by Cornelius de Korte, Solvay Pharmaceuticals, Weesp NL.
To install the contribution, checkout the tag bcdc-v1.0:
git checkout bcdc-v1.0
then read bcdc.README
Usually use extract to install the contribution:
extract maclib/bcdc
##calcphase
Calculate phase of spectrum based on the first complex point of the FID. This is primarily designed for cases in which the first point of the FID occurs exactly at time zero, i.e., an echo. In this case, calcphase may produces answers which are more reliable than aph or aph0.
To install the contribution, checkout the tag calcphase-v1.0:
git checkout calcphase-v1.0
then read calcphase.README
Usually use extract to install the contribution:
extract maclib/calcphase
##compareandplot
compares 2D displays with trace='f1' and trace='f2' for same cross-peaks and plots
To install the contribution, checkout the tag compareandplot-v1.0:
git checkout compareandplot-v1.0
then read compareandplot.README
Usually use extract to install the contribution:
extract maclib/compareandplot
##comparedim
Compare / plot f1 and f2 symmetry equivalents of a COSY-type 2D expansion
To install the contribution, checkout the tag comparedim-v1.0:
git checkout comparedim-v1.0
then read comparedim.README
Usually use extract to install the contribution:
extract maclib/comparedim
##compare
compares 2D displays with trace='f1' and trace='f2' for same cross-peaks
To install the contribution, checkout the tag compare-v1.0:
git checkout compare-v1.0
then read compare.README
Usually use extract to install the contribution:
extract maclib/compare
##convolute
Generates Shifted Laminar Pulses (S.L. Patt, J. Magn. Reson., 96, 94 (1992)) which allow simultaneous excitation of one or more non-zero frequencies with any shaped excitation (including hard). convolute generates shapes in which all excitation frequencies have the same excitation phase, while convolutep allows different starting phases for different frequencies. addshapes adds (convolutes) two different waveforms together.
To install the contribution, checkout the tag convolute-v1.0:
git checkout convolute-v1.0
then read convolute.README
Usually use extract to install the contribution:
extract maclib/convolute
##csll
Produces a line list in a form compatible with CSEARCH from Sadtler (allegedly), using DEPT and 1D spectra.
To install the contribution, checkout the tag csll-v1.0:
git checkout csll-v1.0
then read csll.README
Usually use extract to install the contribution:
extract maclib/csll
##dlli
Creates (and displays) a line listing with integrals for each individual line found. Used also for exporting line listings into the SpecInfo spectral database software. For performing a baseline correction prior to calling "dlli" or "nlli" we recommend using "maclib/bcdc".
To install the contribution, checkout the tag dlli-v1.0:
git checkout dlli-v1.0
then read dlli.README
Usually use extract to install the contribution:
extract maclib/dlli
##dpconi
Trivial macro to start an interactive dpcon display
To install the contribution, checkout the tag dpconi-v1.0:
git checkout dpconi-v1.0
then read dpconi.README
Usually use extract to install the contribution:
extract maclib/dpconi
##drawshape
Draws waveforms (amplitude and phase) on the screen or plotter
To install the contribution, checkout the tag drawshape-v1.0:
git checkout drawshape-v1.0
then read drawshape.README
Usually use extract to install the contribution:
extract maclib/drawshape
##dshpl
displays horizontal plane at cursor position in a 3D data set
To install the contribution, checkout the tag dshpl-v1.0:
git checkout dshpl-v1.0
then read dshpl.README
Usually use extract to install the contribution:
extract maclib/dshpl
##dsvpl
displays vertical plane at cursor position in a 3D data set
To install the contribution, checkout the tag dsvpl-v1.0:
git checkout dsvpl-v1.0
then read dsvpl.README
Usually use extract to install the contribution:
extract maclib/dsvpl
##fpdc
Does "fp" with dc correction on the individual traces
To install the contribution, checkout the tag fpdc-v1.0:
git checkout fpdc-v1.0
then read fpdc.README
Usually use extract to install the contribution:
extract maclib/fpdc
##fpi
Report integral values from arrayed spectra (in analogy to the "fp" command)
To install the contribution, checkout the tag fpi-v1.0:
git checkout fpi-v1.0
then read fpi.README
Usually use extract to install the contribution:
extract maclib/fpi
##getcelem
The macro getcelem analyzes vnmrsys/exp*/acqfil/fid: it returns the number of completed FIDs (celem) and completed transients (ct) in an experiment, which may occasionally be set to 0 after an acquisition, or after stopping or aborting an experiment prematurely. "getcelem" sets them to their correct value.
To install the contribution, checkout the tag getcelem-v1.0:
git checkout getcelem-v1.0
then read getcelem.README
Usually use extract to install the contribution:
extract maclib/getcelem
##getxpk
Extract cross-peak intensities from one or more NOESY spectra, based on a single "manually" measured data set. This material was found in Magnetic Moments, Vol. IV, No. 2, p. 18; corrections published subsequent to that issue are incorporated into the macros.
To install the contribution, checkout the tag getxpk-v1.0:
git checkout getxpk-v1.0
then read getxpk.README
Usually use extract to install the contribution:
extract maclib/getxpk
##lcdatast
Expands the functionality of the "lcdatast" macro to properly adjust the UV chromatogram on the SUN screen for expansions of on-flow or stop-flow measurements (with the standard macro, the UV is always displayed for the whole time of the chromatography). The contribution also makes "lcdatast" label intensities in the UV chromatogram correctly.
To install the contribution, checkout the tag lcdatast-v1.0:
git checkout lcdatast-v1.0
then read lcdatast.README
Usually use extract to install the contribution:
extract maclib/lcdatast
##llbc
"llbc" can be used to apply a "bc" baseline correction to C13 and other spectra with narrow lines and possibly substantial noise, where "region" typically can't be used (or will fail to integrate small signals). "llbc" sets up integral regions based on a line listing (assuming threshold is pre-adjusted), then does a "bc" ("bc(1,80)") before restoring the original integral reset points. For integrating such spectra you may want to use the contribution "maclib/dlli".
To install the contribution, checkout the tag llbc-v1.0:
git checkout llbc-v1.0
then read llbc.README
Usually use extract to install the contribution:
extract maclib/llbc
##loadbiopack
Install utility for BioPack; STRONGLY RECOMMENDED for a smooth installation of "psglib/BioPack" from within VNMR or VnmrJ, see below for instructions.
To install the contribution, checkout the tag loadbiopack-v1.0:
git checkout loadbiopack-v1.0
then read loadbiopack.README
Usually use extract to install the contribution:
extract maclib/loadbiopack
##lsbru
Sets "lp" for data from Bruker "D" series spectrometers (DPX/DRX/DMX, Avance), based on the "decim" and "dspfvs" parameters ("lp" can be 25000 degrees and more with such non-time corrected, digitally filtered FIDs).
To install the contribution, checkout the tag lsbru-v1.0:
git checkout lsbru-v1.0
then read lsbru.README
Usually use extract to install the contribution:
extract maclib/lsbru
##macrocalls
VNMR macro debugging utilities that permit finding macro calls in the specified macro, or macros calling the specified macro. Also recursive searches (for macro calls in submacros, or macros calling a parent macro etc.) are possible. The complete VNMR macro path is taken into account.
To install the contribution, checkout the tag macrocalls-v1.0:
git checkout macrocalls-v1.0
then read macrocalls.README
Usually use extract to install the contribution:
extract maclib/macrocalls
##makehard
Makes various hard pulse shapes
To install the contribution, checkout the tag makehard-v1.0:
git checkout makehard-v1.0
then read makehard.README
Usually use extract to install the contribution:
extract maclib/makehard
##mds
Macros that simultaneously display or plot 1D segments in positions that were previously defined and saved with "s1", "s2", "s3", etc.
To install the contribution, checkout the tag mds-v1.0:
git checkout mds-v1.0
then read mds.README
Usually use extract to install the contribution:
extract maclib/mds
##nph
"nph" is an alternative phasing method for phasing "difficult" data, such as C13 spectra from oil fractions. This method was first published by Larry W. Sterna & Victor P. Tong from the Shell Westhollow Research Center in Houston (FUEL 70, 941 (1991). It can also be used for other spectra, provided they feature a large group of signal at either ends of the spectrum, separated by some flat baseline in-between. This VNMR implementation was first done in 1992 for M. Laenen, Shell, Grand Couronne, France.
To install the contribution, checkout the tag nph-v1.0:
git checkout nph-v1.0
then read nph.README
Usually use extract to install the contribution:
extract maclib/nph
##piv
"piv" acts the same way as "pir", except that it avoids label overlap by writing numbers vertically and offset horizontally if necessary. Related functions "pivn" and "dpiv"/"dpivn" are also provided. This contribution is included with standard VnmrJ 2.2C/D software and with Chempack 4.1 ("chempack/CP4").
To install the contribution, checkout the tag piv-v1.0:
git checkout piv-v1.0
then read piv.README
Usually use extract to install the contribution:
extract maclib/piv
##pl2d
enhanced plcosy and plhxcor macros (broken out from packages.extend); the enhancements include: - added test for running acquisition (to avoid data corruption, see buglist) - avoids overlap of 1D traces with parameters - bugs in 1D scaling fixed - plot area now properly optimized, in particular if no 1D traces are plotted - compatible with other parameter styles (bpa, pap) - 1D experiments do not have to be specified upon first call if they are in default numbers (1H: exp1, 13C: exp2), as described in the manual. - upscaling of 1D traces through an optional argument.
To install the contribution, checkout the tag pl2d-v1.0:
git checkout pl2d-v1.0
then read pl2d.README
Usually use extract to install the contribution:
extract maclib/pl2d
##plot6
plots 3d planes 6 at a time and displays concurrently
To install the contribution, checkout the tag plot6-v1.0:
git checkout plot6-v1.0
then read plot6.README
Usually use extract to install the contribution:
extract maclib/plot6
##savez
a simple macro to autosave fids each bs
To install the contribution, checkout the tag savez-v1.0:
git checkout savez-v1.0
then read savez.README
Usually use extract to install the contribution:
extract maclib/savez
##setdof
a simple macro to set 13C offsets
To install the contribution, checkout the tag setdof-v1.0:
git checkout setdof-v1.0
then read setdof.README
Usually use extract to install the contribution:
extract maclib/setdof
##set_vt
Changes the temperature in a "safe" manner
To install the contribution, checkout the tag set_vt-v1.0:
git checkout set_vt-v1.0
then read set_vt.README
Usually use extract to install the contribution:
extract maclib/set_vt
##stack3d
displays up to 64 3d planes at once
To install the contribution, checkout the tag stack3d-v1.0:
git checkout stack3d-v1.0
then read stack3d.README
Usually use extract to install the contribution:
extract maclib/stack3d
##stack4
displays 3d planes 4 at a time with 3rd dimension labeled
To install the contribution, checkout the tag stack4-v1.0:
git checkout stack4-v1.0
then read stack4.README
Usually use extract to install the contribution:
extract maclib/stack4
##svspec
Saves spectra into files.
To install the contribution, checkout the tag svspec-v1.0:
git checkout svspec-v1.0
then read svspec.README
Usually use extract to install the contribution:
extract maclib/svspec
##useroperator
Examples for "useroperatorlogin" and "useroperatorlogout" macros. These (optional) macros will be called by the "dousermacro" command in "operatorlogin" and "operatorlogout", respectively. They are intended as examples of how a user macro might be used to customize a local installation - there are no manual files, a guide for customization is given via comments in these macros. Acknowledgement: These macros were proposed by Scott Burt, Brigham Young University, Provo, UT
To install the contribution, checkout the tag useroperator-v1.0:
git checkout useroperator-v1.0
then read useroperator.README
Usually use extract to install the contribution:
extract maclib/useroperator
##wndwfunc
window function setup macros
To install the contribution, checkout the tag wndwfunc-v1.0:
git checkout wndwfunc-v1.0
then read wndwfunc.README
Usually use extract to install the contribution:
extract maclib/wndwfunc
##writespec
Writes a spectrum in ASCII format into a file
To install the contribution, checkout the tag writespec-v1.0:
git checkout writespec-v1.0
then read writespec.README
Usually use extract to install the contribution:
extract maclib/writespec
##writetrace
Creates an ASCII file from a 1D spectral trace (f1 or f2 traces from phasefile). A second macro, "writexy", does the same, except that it creates a file with x,y output. A new utility, "import1Dspec" reads 1D ASCII spectra such as from "writetrace" or "writexy" (i.e., Y .. Y or X,Y .. X,Y data) into the current experiment in VnmrJ / VNMR. NOTE: ALL features of this contribution are also found in "bin/harhandler" - if the latter is installed you do NOT need to install "maclib/writetrace" as well.
To install the contribution, checkout the tag writetrace-v1.0:
git checkout writetrace-v1.0
then read writetrace.README
Usually use extract to install the contribution:
extract maclib/writetrace
##xarray
Analogon to the "array" macro, but for entering exponential parameter arrays. Similar to "array" - now a standard VNMR / VnmrJ macro), "xarray" can be called without argument or by just giving a parameter name as single argument, invoking an interactive mode; typically, however, the macro will be used with four arguments: xarray<('parametername'<,#steps,start,finalvalue>)> Note that unlike with "array", the last argument is NOT a stepsize (or rather multiplier), but the size of the last array element; the multiplier will be calculated by "xarray". Example: xarray('nt',10,2,1024) results in nt=2,4,8,16,32,64,128,256,512,1024 and xarray('d2',8,0.1,10) defines an array d2=.1,.19307,.372759,.719686,1.3895,2.6827,5.17947,10 This macro has been recovered from an earlier package contribution by the author, "packages.51/extend".
To install the contribution, checkout the tag xarray-v1.0:
git checkout xarray-v1.0
then read xarray.README
Usually use extract to install the contribution:
extract maclib/xarray
##XT1
XT1 produces a series of displays (w/ optional plots) of exponential decays for crosspeak intensities from a series of hsqcT1 experiments, including F1,F2 values and relaxation times for each crosspeak. Usage: XT1
To install the contribution, checkout the tag XT1-v1.0:
git checkout XT1-v1.0
then read XT1.README
Usually use extract to install the contribution:
extract maclib/XT1
##zoomplot2d
Create a full size plot of a COSY-type 2D spectrum where the noise is left out, and the areas which can have signals are blown up (zoomed) accordingly.
To install the contribution, checkout the tag zoomplot2d-v1.0:
git checkout zoomplot2d-v1.0
then read zoomplot2d.README
Usually use extract to install the contribution:
extract maclib/zoomplot2d