MestRe-C User Guide Megan Bragg 04/14/05

MestRe-C User Guide

Megan Bragg 04/14/05

Some general useful features:

1. You can add Text, Titles, Temperatures, or peak labels (in any font/size/color) to the spectrum. 2. MestRe-C allows you to save files as MestRe-C format for future processing.

3. You can export or print the MestRe-C files in any color scheme or black and white 4. You can add any kind of images to the screen including pasting ChemDraw in spectrum 5. It is simple to import multiple spectra for stack plotting

6. You can view and export an expanded section of NMR spectrum within the same window 7. Can export the data points of the spectrum as ASCII, Meta, LUMASYS, or Binary data 8. All typical phasing, baseline, peak picking, integrating, expansion functions available 9. There are several processing options including: apodization, zero filling, linear prediction,

window functions, high pass filter for solvent suppression, drift correction, HOGWASH, Hilbert Transform, Hadamar Transform, Data Shuffling for Hypercomplex data, Covarience 10. Advanced Processing include: clone selected spectrum, zeroing spectrum, frequency shift,

ability to clean up t1 noise in HMBC, shift spectrum vectors, normalization, smoothing, Douglas-Pecker Interpolation

11. More advanced features include: line fitting (deconvolution), coupling constant analyzer (1st order multiplets only), suppress diagonal cross speaks (2D), symmetrize, tilt or transpose real square mix, and data analysis

12. You can write a “script” for processing several spectra identically. You just process one a certain way and then run the script for the rest to be processed the same way (kinetics).

Additional Menu Options:

1. From File: import multiple spectra (must have “import into same window” checked), exporting file in different formats, and file transfer options

2. From Edit: Change 2D contour colors, entire palette colors, and copy the file in a few “non-meta file formats”

3. From View: Add/Remove Toolbars

4. From Process: Zero Filling, Linear Prediction, Symmetrization, Tilt, and many more processing options

5. From Tools: Data Analysis, Measure Coupling Constants, Coupling Constant Analyzer, Arithmetic (Add/Subtact/etc. Spectra), Line Fitting

6.

From Options: settings, properties, script editor

First Time Use:

1. Push the F1 key for a help manual – this is very brief but will help

2. Add the 2D toolbar by going to View Æ Toolbars Æ 2D. It does not immediately open when starting MestRe-C.

3. If you try to import your FID but can’t see it in the folder, remember to change file type to “all files” because sometimes MestRe-C will initially only see MestRe-C files. Also remember that

Varian 1D and 2D as well as Bruker 1D are called “FID”; however, Bruker 2D are “SER”

4. Go to: Options Æ Settings and change the number of “undo” steps to “1”. Notice while you are here that you can choose to print the spectrum in color, view grids or printable area, and change screen color.

5. After you import the FID for the first time, go to: Options Æ Properties and click through the parameters you can change on the left side of the window. You can generate a new style with your own preferences. Some useful changes to make are:

A. If you want your data parameters displayed on the screen, go to “spectrum” and click “show parameters” you can edit which parameters here also.

B. Go to “Vertical Scale” and un-click the box that says show vertical scale.

C. Go to “Horizontal Scale” and notice that you can change the units, increase the tics, etc. D. For 2D spectra, there are automatic borders which make the spectrum look weird. Go to “Slices” and click on the Borders button and set it to “none”. Do this for the both borders. E. If any part of your scale is ever cut off when you try to print it, go to that scale and increase the “size” next to location, this will move the print border farther away from your spectrum. F. Later, you may or may not want to display the peak picking on the screen – you can directly export it so you don’t have to display it. Go to “peak picking” and un-check the display box. You can also change decimals at this point. Remember if you do this that you

won’t see the peaks when you pick.

G. Later, you can choose not to show your curves on the screen because this can make the spectrum harder to read. Go to “integration” and un-click “show curves”.

5. When you import multiple spectra for say a stack plot, be sure to click “import into same window”. Once you have imported them and pushed the button to stack plot them, you can hold down shift and select all of them and process them the say way (Or expand at the same time). 6. Click on the spectrum and hold down the mouse button, you can move the spectrum closer to the scales.

7. Four little bugs I’ve noticed that hopefully will be fixed in future versions:

A. If you are going to expert to a “Word” document, open the word program and then go to MestRe-C and push the “copy to metafile button”. If you do that in reverse, the image does not always copy.

B. If you export a colored metafile into a dark background “PowerPoint” presentation then the scale is not visible. To get around this, I change the scale color to “silver” so it is visible. You can also paste into word and then copy and paste into PowerPoint if you have problems with the spectrum.

C. Do not add images until you are done with the spectrum because the program will not let you undo after you add an image. Also, save the spectrum before you add the image.

D. Don’t increase the “Size of Complex Points” when you “ft” the spectrum unless you know what you are doing because if you increase it too high, you will freeze the program and likely your computer.

Using the Toolbars

Top Horizontal Toolbar (for typical processing):

-

Opens files so you can open/import your fid

-Transfers your NMR data from the spectrometer.

- You can print directly from MestRe-C.

-Print Preview before you copy or print the spectrum

-Copies the Spectrum as a metafile image to transfer to applications

-Increases and Decreases the size of the peaks

-View entire spectrum while you have a portion expanded.

(Not for pasting

with the expansion in the window, a later button does that)

-Expand spectrum

(pull down menu reverses the expand)

-Allows specific expansions at numerical intervals

-Returns expanded spectrum to full spectrum

-Expands or Decreases from the center of the screen

-Moves entire spectrum any direction with mouse (hold)

-Fits the intensity of the spectrum so all peaks are shown

-Used for 2D phasing to pick a point for phasing

-Click on any peak for all information on it

-Add a text box to the spectrum

-Fourier Transform your FID

(pull down menu allows SEVERAL specific options for Fourier transforms including linear Prediction options and filling, apodization, functions, protocol, corrections, other options)

-Phase your spectrum

(manual allows both coarse PH0-zero order-and PH1-first order- as well as fine tuning, moving center of the phase, reset; auto pull down menu allows four different types of autophasing. For 2D phasing choose manualÆ 2D phasing with 1D slices then use the tool for picking point for 2D phasing – the plus sign – and add traces to the box – you can phase in both f1 and f2 dimensions )

-Baseline correct your spectrum

(pull down menu allows automatic baseline correction for 1D and 2D –chose full auto correction- as well as Bernstein, polynomial, multipoint, trigonometric, and manual)

-Reference your spectrum

(includes several typical references and allows addition of more references)

-Peak picking, use by dragging cursor over peaks depending on

how many you want, you may need to expand or do it “peak by peak” (pull

down menu allows a very important feature under list peaks: EXPORTING all the peaks you’ve picked into a text document so you don’t have to type the numbers up!!! Additionally, another important feature is that once you’ve picked a peak, a text comment can be added beside those peaks – so you can label your peaks with respect to the molecule. You can also show correlations to H or C spectrum and delete all of the peaks labels at the same time

-Integrate the spectrum –

Drag cursor over peak the distance you want to integrate you can expand during this integration and it doesn’t affect the integration – double clicking on the integration allows for reference integral to be set

.

(Pull down menu allows a very important feature under list integrals that allows the integrals to be exported as ASCII or XLT files for further processing. Additionally, the integration manager allows specific resizing of already drawn integrals, navigation through the integrals, deletion of integrals, as well as manual and auto bias and slope correction.)

Bottom Horizontal Toolbar (for one of more spectra on the same screen):

-Align Spectra with the dominant Spectrum

-Centers one to several Spectra on the screen

-Resizes spectra with the dominant Spectrum

-Superimposes two or more spectra

-Send one spectra to back or front of layer

-Tile spectra on screen

-Stack plot

(pull down menu allows specific angles of stacking to be chosen as well as manipulation of viewing parameters)

-After you expand, click this button to add the expansion above

your full spectrum as an image that is copied.

As long as the small window is highlighted, all tools apply to this spectrum, click on large window to apply all tools to it.

-Play/Stop FID or script that you already set up

Vertical Toolbar (for 2D/3D)

-plotting mode

(Pull down menu allows several plotting styles. Choose “fast” for processing and change the mode for printing –specifically contour plot copies entire screen as “black and white”, filled contour plot copies entire screen with colored cross peaks.)

-3D processing

-Removes/Adds Positive Levels

-Removes/Adds Negative Levels

-Add traces to 2D spectrum

(pull down window allows several different types of traces to be applied. For plotting purposes, you want to paste processed proton and/or carbon spectrum, so choose: setup 1D traces Æ from file and get them from your file).

These Remaining tools move and expand the traces once applied to

the spectrum.