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Appendix


CHAPTER 21: Frequently Asked Questions

21.1 How are the CCBond, FRED, and NMRanalyst programs related?

Our research program of the automated 2D INADEQUATE spectral analysis was called CCBond (Carbon-Carbon BOND).1 Varian, Inc. marketed it under their trade name FRED (Full Reduction of Entire Datasets). After extension to the analysis of standard 2D and 3D NMR spectra, we renamed the software to NMRanalyst.

21.2 Any differences between MS Windows and LINUX NMRanalyst?

The following subsections describe the minor differences.

21.2.1 Backgrounded Computations Killed on Logout

NMRanalyst allows backgrounding computations. On Linux, backgrounded computations run to completion even if the user logs out. Microsoft (MS) Windows kills user processes on logout.

21.2.2 Directory and File Names not Case Sensitive

On Linux, file and directory names are case-sensitive. MS Windows file systems are case preserving, but not case sensitive. A new file called "Data" overwrites an existing file called "data" in the same directory. NMRanalyst default names are unique and work as expected on case-insensitive file systems. When choosing new names, make sure they differ by more than the capitalization.

21.2.3 Handling of File and Directory Access Permissions

Linux provides read, write, and execute file permissions for the owner, group members, and other users. MS Windows uses different kinds of file systems with different access permissions. On NTFS,2 all files have an owner, group (which is not set by default), and access control list (ACL) permissions. Windows NMRanalyst maps the MS Windows file access permissions to the closest Linux settings.

21.2.4 No Special Characters Allowed in Path or File Names

Microsoft Windows allows special characters in directory and file names which can cause problems for the UNIX Shell started from NMRanalyst. Avoid the use of special characters (such as a plus sign, comma, semicolon, equal sign, or square bracket) in file and directory names which cause problems when used unquoted in a UNIX shell.

21.2.5 Microsoft Windows Drive Letters and UNC Path Names

Linux systems organize files in a single tree-like file system of directories. Microsoft Windows typically has several file system trees distinguished by a letter of the alphabet, the so-called drive letter. Windows NMRanalyst specifies the drive letter (e.g., "C") as part of the path name in the format "C:/some_pathname". To change to a different drive letter from a NMRanalyst filebox, type the new drive letter in the Enter path or folder name input field, and click the [Update] button to update the Folders and Files lists.

To access network filesystems, the MS Explorer can map network resources to drive letters. Another way is to use the uniform naming convention, UNC. UNC paths start with two slashes and consist of server name, share name, directory tree, and file name like in:

 //myComputer/home/ANALYST.WIN/VERSION

While Linux uses slashes ("/") to separate directories in path names, MS Windows uses back-slashes ("\"). NMRanalyst accepts both notations and converts specified back-slashes in UNC paths into slashes.

21.2.6 Incorporation of a License Server in Windows NMRanalyst

We offer a time-limited evaluation version of Windows NMRanalyst. A license server in this software causes the 1D analysis, nD analysis, AssembleIt, and NMRgraph programs to stop functioning when the $NMRDIR/license.dat file is not correctly installed (left figure) or when the evaluation time period has expired (right figure). The Windows NMRanalyst is also available for permanent installations not using this license server.

21.3 How can I access Linux files from a PC running MS Windows?

If the computers are not networked, then write a DVD or other medium on the Linux side and load it on the PC. To copy individual files over a network, start the ftp program on MS Windows with [Start] [Run...] and specify

 ftp computer_name

Log in, type "bin" for binary mode, and use "get filename" to copy the "filename" file to the PC running MS Windows. If files from the Linux computer are accessed frequently, install the free Samba software on the Linux computer. The Samba software with documentation can be downloaded from http://samba.org. Configure Samba to allow the PC (or several PCs) direct access to specified Linux file systems. For example, acquired NMR data from the Linux side can be accessed directly from the PC without having to copy these files or directories to the PC and NMRanalyst results can be written directly to the Linux file system. Another useful Samba feature is printing from the PC to printers on the Linux side.

21.4 Can I run NMRanalyst on an Apple Macintosh?

Dr. Dimitris Argyropoulos (Varian Germany) tested Windows NMRanalyst on an Apple PowerBook G4 running Mac OS 10.2.2 and Virtual PC with Windows 2000 Professional. Virtual PC involves the emulation of an Intel processor. So Windows NMRanalyst becomes several times slower than running natively on an Intel processor of similar speed. But it functions as expected.

21.5 How to display new MS Windows applications as foreground windows?

Microsoft enabled a Windows feature by default years ago: Applications were not allowed to display foreground windows (or new foreground windows were not recognized as belonging to the current foreground application). When starting a new NMRanalyst UNIX Shell, Help, NMRplot, or NMRgraph window on such Windows versions, the new window was shown below other displayed windows. The application would then flash in the taskbar (3 times by default) indicating this window was denied the privilege to be displayed as a foreground window.

Newer versions of Windows no longer interfere with the operation of NMRanalyst and its sub-windows. On MS Windows systems still showing this problem, download the TweakUI application from Microsoft's web site: http://www.microsoft.com/windowsxp/downloads/powertoys/xppowertoys.mspx. Follow the instructions for installation. Start TweakUI from the Control Panel, select the [General] tab, and deselect the [Prevent apps from stealing focus] checkbox.

21.6 Any UNIX editor available from the Windows UNIX Shell?

The Notepad (started with: [Start] [Programs] [Accessories] [Notepad]) and WordPad are the native MS Windows editors. The NMRanalyst UNIX Shell offers an enhanced vi editor for "UNIX style" editing.

21.7 How to copy and paste text in Windows NMRanalyst?

To copy text, select the text with pressed left mouse button. NMRanalyst's [Edit] [Copy] menu item copies the selected text into the CLIPBOARD. To paste the CLIPBOARD contents into a MS Windows program, an NMRanalyst input field, or the UNIX Shell, simultaneously press the keyboard [Shift] and [Insert] keys. In the UNIX Shell, holding [Shift] and clicking the left mouse button works as well. The only known limitation is that the UNIX Shell may hang when text containing UNIX line endings (e.g., multi-line Windows NMRanalyst output screen text) is pasted into it.

21.8 What should I do about the Windows XP NMRanalyst security alert?

Starting NMRanalyst under Windows XP may cause the shown security alert. A similar security alert may result from starting the FindIt Database Manager of the NMRanalyst application. NMRanalyst communicates with NMRgraph and NMRplot through sockets to handle printing plots, displaying help information, and aborting adding user structures to the FindIt database. No network connection is ever attempted. Click [Keep Blocking], NMRanalyst continues to function properly and this popup won't show again.

21.9 How can I get NMRanalyst printing to work?

On Red Hat Linux, from the desktop Main Menu, click [System Settings] and then [Printing] to display the name and state of known printers.

On MS Windows, select the Start menu [Settings] item [Printers] item. The displayed Print Manager window shows an icon for each known printer. If none is displayed, see the Windows help system on how to add one. If several printers are accessible from the PC, first notice which printer is currently selected as default to reset this setting later. Now click on the icon of the desired printer with the right mouse button, select [Set as Default Printer]. Right click the selected printer icon again, select [Properties] item, and click [Print Test Page] button. If the selected printer does not correctly print the test page, follow the Windows help system suggestions.

Start NMRanalyst (if not already running). Select [File] menu [Print...] item to start its Print Settings popup controlling all NMRanalyst print settings. Set the "To:" option menu to the appropriate print format. For a Windows printer, select a printer driver named closest to the printer name. If none of the listed printer drivers matches the desired printer, choose Other Printer from the option menu to invoke the Windows native dialog for printing. For Linux, try the PostScript Printer setting. Delete the input field entry on this line and click [Apply Settings]. Now display the Print Settings popup again and this field contains the default printer name. If on MS Windows it is LPT? or COM? (with a number instead of the question mark), it is a printer attached to the local PC. If on MS Windows it is a shared printer connected to another PC on the local network, or a Samba exported share from a Linux system, the printer name has the format //computer_name/printer_name. (NMRanalyst changes Windows backslashes to regular slashes.) Make sure this computer_name can be reached over the network and printer_name corresponds to a shared printer. On Linux, printer names from the Print Manager can be used directly whether they are locally or remotely attached.

If the current workwindow output screen contains text, print it by clicking the [Print] button in the NMRanalyst Print Settings popup. Otherwise specify any text file in the Print File: field and print it. If the resulting page is printed but contains formatting instructions or graphic symbols, select a more appropriate printer driver. The printer settings are saved (in file .analyst) and are used for future NMRanalyst printing until explicitly changed. You may reset the PC default printer setting above if it was changed. In case of further printing problems, save PostScript files to disk and find a way to print them.

21.10 How can I capture NMRgraph and NMRplot displays?

On MS Windows, display the desired plot and copy the whole screen contents onto the clipboard by pressing the [Print Screen] keyboard key. Then start a drawing program (such as [Start] [Programs] [Accessories] [Paint]), paste the clipboard content in the drawing area, crop the image as desired, and save the image into a file.

On Linux, capture the screen image with the X Window dump utility and select the window to be captured by clicking on it:

 % xwd > /tmp/p.xwd

The captured screen image can be displayed with "xwud < /tmp/p.xwd&". This might be required for applications which cannot directly capture nmrplot OpenGL images. To obtain a higher than screen resolution, save the NMRplot or NMRgraph display in a PostScript file: [File] [Save PostScript...]. To create a 200 dpi 2800x2800 pixel image from the vector graphic PostScript file, use (type the command as a single line):

 % gs -dNOPAUSE -dBATCH -sOutputFile=myFile.jpeg -r200
 -g2800x2800 -sDEVICE=jpeg myFile.ps

21.11 Why can't I switch NMRanalyst to a different spectrum type?

NMRanalyst does not allow changing the spectrum type while computations are in progress. Workwindows with ongoing computations are identified by the clock icon on their folder tab. Either wait for the remaining computations to finish, or join each active workwindow and terminate the computation by clicking [Stop]. A new spectrum type can be selected after the last computation terminates.

21.12 Why are the NMRplot colors wrong?

NMRanalyst, NMRgraph, and NMRplot are Java applications and are displayed on Linux operating systems by its X Window system. NMRplot itself uses a small number of shared color cells. So it does not interfere with the operation of other running X Window applications. But if another running application reserves a large number of color cells for its private use, other running applications have to share whatever color cells are left. To resolve NMRplot color problems, exit the application reserving the available color cells. If Varian VNMR or VnmrJ are displayed on your X Window system, they likely cause this problem. Exit them to free over 80 private color cells. Then start NMRplot and it shows in its intended colors.

21.13 How to fix incorrect NMRplot or NMRgraph rendering?

Problems with the NMRanalyst graphic rendering are typically caused by the window system or graphic card configuration.

On Microsoft Windows, the color of a displayed NMRplot image may change during mouse interactions or window resizing. A NMRplot display may not redraw correctly when overlapping with other display windows. Random dots may appear on a NMRgraph display. Should incorrect rendering of NMRplot or NMRgraph occur, decrease the number of bits of color information stored for each screen pixel and decrease the hardware optimization level. From the MS Windows Control Panel, double click the Display icon. Select the [Settings] tab and reduce the number of bits used for each screen pixel from the Colors option menu (e.g., from True Color (32 bit) to High Color (16 bit)). Click the [Advanced...] button, select the [Troubleshooting] tab, and drag the Hardware acceleration slider to None. Click [OK] to apply the settings.

On Linux, black lines from the edges of moved atoms or correlation lines may remain on an NMRgraph display window. To remove such artifacts, click the right mouse button over an empty space on the desktop. From the displayed menu select [Refresh Desktop].

21.14 How to increase the paging space on Linux?

To overcome limitations of available physical memory, Linux uses virtual memory (hard disk space, often called paging space or swap space). The following table describes adding an additional 100 MBytes of paging space on Red Hat Linux.
Operating System Task and UNIX Command

Red Hat Linux

List all paging spaces:

/sbin/swapon -s

Create new paging file:

/bin/dd if=/dev/zero of=/swapfile bs=1024 count=102400

/sbin/mkswap /swapfile

Activate paging file:

/sbin/swapon /swapfile


Modifying the system paging spaces requires root privileges. To permanently make this modification, edit /etc/fstab to include:

 /swapfile        swap        swap    defaults    0 0

21.15 How to specify correlations for the AssembleIt structure generation?

AssembleIt generates possible molecular structures from correlations (carbon-carbon, nitrogen-carbon, etc.) contained in a specified *.plot file. These correlations are typically created by combining NMRanalyst spectral analysis results. But correlations obtained from publications and other means can be saved in a *.plot file which can be used for the molecular structure elucidation.

To create the *.plot file with the molecular structure editor NMRgraph, display an existing *.plot file. Delete all its atoms and correlations. Enter the desired correlations. Set the atom type and number of free (non-hydrogen) valences from the Atom Property Editor. Set correlation types from the Correlation Property Editor. For correlations which are known to be bonds (such as derived from INADEQUATE or 1,1-ADEQUATE), use the correlation settings:

Bond Type: [Single], Line Style: [Solid], Arrow: [Both].

For ambiguous correlations, such as derived from HMBC or DQF-COSY, use:

Bond Type: [Single], Line Style: [Dotted], Arrow: [Both].

Save these correlations in a file such as new.plot. In the AssembleIt workwindow, deselect [COMBINE NMR ANALYSIS RESULTS], select [AssembleIt: ELUCIDATE MOLECULAR STRUCTURE FROM NMR DATA], specify in the Input: Atom-Atom Corrections field the created new.plot file. (If the field is not visible, select [Edit] menu [Preferences...] item, set Mode: to [Full NMRanalyst], select the [Show All Input Fields] switch, and click the [OK] button.) Set the structure generation options, and run the workwindow.

1Dunkel, R., Ph.D. Thesis, University of Utah, 1990.

2NTFS is the native file system for Windows 2000, XP, and Vista.



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