Index:
The Pronto program currently contains five different report facilities. They will be described below. The list of reports available is accessible from the Report menu in the Tools menu from.
This report is used to generate condensed reports, presenting all chemical shift values for the atoms in an amino acid residue. The information is presented in one line per amino acid.
The setup window for the spin system report is shown in Figure 1. The browser at the top contains an entry for each axis in each spectrum, whose information is to be included in the report. It is thus not only possible just to print out chemical shift values from selected spectra, but also from selected axes. Add the spectra from the spectrum window, and step between the axes by pressing the button to the right of the spectrum name field. If you want all chemical shift information from a spectrum, include it as many times as it has dimensions, and select a different axis for each line in the browser. The Output Format can be either Plain ASCII File or WordPerfect 5.1 format. The PostScript format is currently not implemented. The WordPerfect 5.1 files contain neither printer setup nor font information. After setting the printer and fonts in WordPerfect, it might be necessary to change the tab settings in the document. The file contains the necessary codes for decimal alignment of the numbers, the atom names are presented in Greek letters, and lines with excessive information are broken into several, indented lines.
The sequential effects are displayed in a diagram, where each column position corresponds to a position in the amino acid sequence. A sequential NOE between a set of protons in two amino acids within a specified distance in the sequence is displayed as a horizontal bar between the columns with the two amino acid residues.
The main setup window for this report is shown in Figure 2. The Plotter file parameter is used to specify the name of the file to contain the commands to the plotter or laser printer producing this report. If a non-hardcopy device is chosen, this parameter has no effect. The Device name selects the output device. Currently, the following devices are supported on the Personal Iris:
X11: Create the output in a X11 Window.
GL: Produce the output in a GL window. This currently does not work across a network.
HP7550: Produce output for a HPGL plotter. The output may also be printed on a Hewlett-Packard LaserJet III printer, in HPGL mode, if the printer is equipped with a RAM expansion and the Page Protection is selected.
HPLJSII: Produce output to a Hewlett-Packard LaserJet II printer, 300 dpi. You may need a minimum of 1.5 Mb of memory in the laser printer to use this driver.
HPLJIII: Works as the HPLJSII driver, except that the bitmap output is compressed using the methods supported by a Hewlett-Packard LaserJet III printer. You may need a RAM expansion board for the printer to use this driver.
PS: Output to a PostScript printer is produced.
Further drivers may be supported in the future.
The Chain ID selects the amino acid chain to be plotted. Each diagram can only contain residues from one chain.
The Number of first amino acid and Number of last amino acid fields are used to limit the report to a subrange of the sequence. This is particularly useful for large proteins, where the whole plot may not fit the paper. The Number of amino acids per line field selects how many residues that are displayed on each line. If this value is set too low, the number of lines necessary to hold the selected part of the sequence may be too big to fit the paper, and if it is chosen too high, the lines may be too wide for the paper. The Character height, cm. selects the size of the characters. Pressing Make Report starts the generation of the plotter file or the output to the screen. The button will remain highlighted while the output is being generated. Closing the windows for the X11 and the GL driver is done by clicking with the mouse inside the window. The user must copy the output file produced by the hardcopy device drivers to the appropriate device or to a printer queue handling the device.
Note: If the fields in the amino acid catalog containing the one-letter code for the amino acid is blank, no text with the amino acid name will appear.
The bottom part of the window is a scrollable list of the selected sequential effects to be displayed. A new effect is created using the Add Line button, and a current effect can be selected using the mouse. The current effect can be removed using the Remove Line button. The list is set to a useful set of examples using the Add Defaults button. An entry in the browser can be inspected by pressing the line in the browser. The zoom window for this function is displayed in Figure 3. Changes in the window only take effect if the Accept button is pressed, if Cancel is pressed, the window is closed without changing anything. The Sequence difference fields define the distance between two amino acids considered, i.e. if a daN(i,i+1) effect is to be plotted, this field must be set to 1. The First atom name sets the name of the atom in the amino acid with the lowest residue number, and Second atom name sets the name of the atom in the amino acid with the highest residue number. In the above example, the first name should be HA, and the second name HN. Specifying HA will match any proton name starting with the two letters, H and A, i.e. the protons: HA, HA1, HA2, and HA#.
The Color selects the color of the bar to be drawn, and Fill density selects the density of the filling of the bar.
The contouring report facility generates an input file for the mcnt program. The mcnt program can display contours from one or more spectra in one or more windows, either on the screen or to a hardcopy device. The contouring report facility currently has three ways of presenting contour diagrams:
1. Plot of the whole or a part of one or more spectra. 2D spectra are normally plotted in 1x1 ppm areas, one per page, out of the chemical shift range selected. The plots can be annotated with information about the cross peaks. 3D spectra are plotted as one plane at a time.
2. Plot of all spin systems, using 2D spectra. Each page printed contains one spin system, presented in "cathedral windows".
3. Plot of spin systems, using 3D spectra. This is useful for plotting spin systems in a 15N-HMQC-TOCSY spectrum. Each page contains three bands. The center band has the plane number of the 15N atom, the center y value of the HN atom, and an x range selected by the user. The planes above and below are plotted in two bands, one above and one below the center band.
The setup for the cross peak report facility is displayed in Figure 4. The setup of the contouring is done in the contouring setup window, and saved as a setup in that window. The setup is selected and transferred into the report window by pressing the Contouring Setup button at the top. This defines the spectra to be plotted, the contour levels, the colors, and the degree of annotation of the cross peaks. The output format is selected by the Output Format field: Select among the three formats as mentioned before. The Destination and Options fields are only used, if the output is directed to a spooler queue. This requires a queue setup with a proper interface file that pipes this file through the mcnt program. If these fields are blank, the input to the mcnt program will be written to the file named in the Output Filename field instead. The Device name field contains the name of the device to be used, as listed for the sequential NOE effect plotter. You can specify a device producing output on the screen, however, this is not useful: Use the facilities in the contouring window instead.
If the Emulate color is set to On, gray shading will be used on the laser printers to emulate colors. If Pen plotter is selected to On, the pen movements will be optimized to terminate plotting of one whole contour line before moving to a new contour line. If the HPGL file is plotted using a laser printer, the selection Off will speed up the plotting.
If Plot Regions is selected as Output Format, the information in the range part of the setup window is used as follows: If 3D spectra are included in the setup, the Min plane field specifies the number of the first plane to be plotted, Max plane the last plane, and Step plane the number of planes to step between each set of plots. The planes are numbered from zero to the number of planes minus one. This is ignored for 2D spectra. The x and y ranges are used both for 2D and 3D spectra. The Min x is the lowest chemical shift value plotted (specified in ppm), and Max x the highest, in the x direction. The mapping between plotter axes and spectrum axes is taken from the contouring setup. The x axis of each plot produced will have a width of Step x ppm. The same applies to the y axis fields. Thus, if a 3D spectrum is included in the contour setup, a total of 64x12x12 plots will be produced! Normally this value is much lower, as you would plot out the whole sweep width in the x and y dimensions for 3D spectra, and, of course, only one plane from a 2D spectrum. E.g., to plot out the whole sweep width for a 15N-HMQC-TOCSY spectrum, select 6 for Min y, 12 for Max y, and 6 for Step y, if y is the HN axis, and -1 for Min x, 12 for Max x, and 13 for Step x, if x is the all-H axis.
If Plot Spin Systems is selected, only the Step x and Step y values are used. They will select the width of each of the "cathedral windows". A value of 0.2 ppm is normally a good value to start with.
For Plot 3D Spin Systems, Step x and Step y select the width and height of each of the bands plotted.
If Plot Setup is selected, all ppm ranges are taken from the Contouring Setup.
Selecting Plot Sequential Assignments to plot strips of spectra for each spin system next to each other. Fill in the Sequential Assignment at the bottom, and the number of spin systems to plot on each page.
Pressing Make Report will start the generation of the input file to the mcnt program. This button will remain highlighted while the file is being produced. As soon as the file is generated (either as a file in a directory or as an entry in a spooler queue), changes can be made to the database without affecting the output produced by the mcnt program.
The setup window for the cross peak report is shown in Figure 5. The output is produced for one or more spectra. The report contains a line for each cross peak in the database for that spectrum. Each line contains the chemical shift values, intensity value and class, assignments, and possibly the coupling constants and integration limits. The output can be made in an ASCII file or a WordPerfect 5.1 file. The PostScript format has not been implemented.
The distance restraints report is used to transfer distance information from Pronto to structure calculation programs. Currently, output can only be produced in X-PLOR format. The setup window is shown in Figure 6. The browser at the top contains the spectra whose peaks are reported. The Output Filename contains the name of the file produced. The file is written in the $PRONTO_WORK directory. In the Residue relationship you can choose if you want inter-residue distances, intra-residue distances, or both. The intensity class stored in the cross peak catalog is mapped into a distance interval using the table at the bottom of the window. You can also choose to make a distance file with a selection of the intensity classes. The four values in each row are interpreted as follows:
1. The upper interval, in Å.
2. The lower interval, in Å.
3. The equilibrium distance, in Å.
4. Value added to distance, if one or more of the protons refer to a methyl group.
The whole interval for non-methyl protons is thus from [3]-[2] to [3]+[1].
Currently, the only way to classify NOE peaks is to inspect each peak manually and enter the intensity class in the cross peak zoom window.
The NOE statistics report is used to count the number of NOE's and store the information in a file.
The default is to generate a NxN matrix, where N is the number of residues. Entry Aij contains the number of NOE's between residue i and j. You can choose to omit counting the inter- or intraresidue NOE's.
Enter the spectra from which to obtain cross peak information in the list at the top.
The output is suitable for import in a spreadsheet program. Select "Matrix form(CR/LF)" to make the file readable from PC software without conversion. You can also select the output format "Linear form" in which each entry Aij in the matrix is written on a line of its own, preceeded by the indices i and j.
Press Make Report to start the analysis. The output file is stored in the $PRONTO_WORK directory by default.
The purpose of this tool is to export an atom list with corresponding ppm values. The list is written in a format suitable for the "total.f" program, written by Mike Williamson et al.
This program is available from ftp://ftp.shef.ac.uk/uni/academic/I-M/mbb, and is described in M.P. Williamson and T. Asakura, J. Magn. Reson. Ser B, 101 63-71, 1993.
Add the spectra for which you want ppm values to the list at the top.
Enter the name of the Output Filename. $PRONTO_WORK is the default directory.
The protein name must match the name specified to the "total" program. Length is restricted to three characters.
Press Make Report to start.