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Use of Silicon Graphics Workstations


Silicon Graphics Indigo workstations are intended for use with molecular modelling and molecular biology, programming and 3D visualisation of data produced during project work, performing crystal structure database searches, use of the Mathematica program and for electronic-mail. As you enter the department you will be automatically registered for these systems
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Login on to a Workstation

Check that the workstation monitor is switched on (the green light glows when it is) and move the mouse around to deactivate any "screen saver". Type your user identifier, normally something like BLOGS or JB1, then press the key located above the shift key on the right hand side of the alphabetic keys. Enter your password in a similar manner. If these are accepted the following display should appear. If the login fails, check carefully that you have typed everything exactly as shown on the registration form. Both identifier and password are "case sensitive", If a capital letter is indicated, you must press the shift key to enter it.

You will be left with the Console window and what is called the "toolchest" menu. Most of what you will need to do can be initiated from these two areas. In the instructions that follow, a click from say the left hand button of the mouse will be indicated by a <=.
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Window Management

At this point you should be aware of the conventions surrounding "window management" and how to activate or "focus" a window. Since many windows can be "open" on a screen at any time, certain rules for moving between them and managing them have evolved.

The department of Chemistry has adopted the standard that the "active" window is seen in its entirety, and "inactive" windows may be obscured underneath as seen in the example above. The top window is said to be "raised" with respect to the bottom. The bar on top of an active window is seen blue. To make a window "active", a single mouse click is required with the left hand button. Only when a window is active will anything typed in from the keyboard be associated with that window. The keyboard is said to be "focused" on the window.
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Resizing and Finding Windows

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The Console Window.

This is used for "command line" style interaction with the UNIX operating system of the workstation. In particular, errors and messages from the system appear in this window. Note that the default state of this window is "minimised", and that to make it usable, it has to be expanded by clicking in its area with <=.
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The Toolchest Menu.

This residues permanently on the left hand side of the screen. It serves as the primary menu for all documentation and applications specific to the chemistry department.

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These are available by clicking with <= on Applications in the Toolchest menu. The main applications available are; SYBYL, MacroModel, Explorer, Quest (X-ray) and Mathematica.

To illustrate a typical application, the procedure for invoking MacroModel is shown here. Move the mouse cursor over from Applications to MacroModel and release. After a few seconds, a mobile outline of a new window appears on the screen which has to be "placed" somewhere on the screen by moving the mouse cursor and clicking with <=. You will probably want to place it near the top left of the screen. Identify the terminal as 2 (3D Silicon graphics) and press the key. If on a Macintosh using MacX, or if you are connected to a remote Indigo (see 3.4.3) identify as 1 (2D X Windows) and press the key. Several more windows will appear automatically, ie they do not need "placing". To exit from Macromodel, select STOP in the buttons menu.

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This represents a sophisticated 3D visualisation tool which can be customised for almost any application. One such "object oriented tool" already present is labelled HORBS. Its prime use is to visualise hydrogen orbital wavefunctions which have previously been calculated from a custom program written as one of the projects in the programming course. This module takes a simple file containing numerical data and "visualises" it in three dimensions. Numerous other modules are available.

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Math Notebooks

Mathametica is another visualisation package for numerical processing. Run one of the pre-programed noteboooks from the application menu. You can also try one of the following functions at the Mathematica prompt;
Plot3D[Cos[Sqrt[x^2 + y^2]]*Exp[-Sqrt[x*x + y*y]/5],

Plot3D[0.5x^2 + 0.5y^2 +0.8/Sqrt[(x+0.2)^2 + y^2] +
0.2/Sqrt[(x-0.8)^2 + y^2],{x,-1.5,1.5},{y,-1.5,1.5},
Plot3D[Sin[x] Sin[y] x y,{x,-Pi,Pi},{y,-Pi,Pi},PlotPoints->50]
The last plot produces effects similar to Explorer, although unlike the latter, the image cannot be rotated in real time. You can of course enter your own function in a similar manner.

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This item invokes a so-called World-Wide Web browser. The currently preferred browser is called Netscape, although other programs such as Mosaic or WebRouser are also available. From this starting point, you can browse the departmental information systems, or go further afield! Already in 1995, many sources of chemical information on the Internet were available, which if you have time you may wish to explore. A good starting point is here or here.

Note about use of the World-Wide Web: Please note that you should use the World-Wide Web responsibly. There are a number of sites out there in "cyberspace" which contain material that by no stretch of the imagination could be construed as being appropriate for a chemistry course. If you are seen displaying offensive or inappropriate materials, this could result in disciplinary action being taken. Please consult the code-of-conduct which should be available on the computer room walls for further details.

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The next item in the Toolchest menu shown above enables you to connect from the workstation you are currently working on to another such system. You may wish to do so because the "CPU" on your own machine may be working hard at a problem, leaving you with a slow response. By connecting to another computer which may be idle, you could take advantage of the capacity on that machine. It is possible also that particular programs with restricted licenses may only be available on one particular machine, or that another machine has some hardware facility that your own system does not. After selecting a workstation, you will be asked to login, and a console type window on the remote machine will become available.
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Login From a Macintosh or Microsoft Windows PC.

These devices are normally connected to the ethernet and must have a suitable program implemented such as Telnet or X-Windows.
Using X-Windows.
The windows that can be created directly on a workstation screen can also be "exported" across a network and appear on a Macintosh screen. To do this, a program called MacX must be running on the Mac. To create the file editing and terminal window using MacX, run edit-a-file from the Remote workstations menu. Whilst graphically non-intensive tasks such as editing a performed perfectly adequately, those that require high performance graphics, such as Explorer, cannot be invoked in this way.
Using Telnet.
This really represents a sub-set of what is possible under X Windows. Only the equivalent of a console window for the Indigo workstation can be created on the Mac. Nevertheless, it is useful for finding out what files you have etc, provided you are prepared to enter Unix style command lines.
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These are useful functions you may wish to invoke any time whilst running another program.

File editor.

Used to create new programs and datafiles as part of the programming course.

Invoke Edit-a-file, whereupon the outline of a new window appears which has to be "placed" by clicking with the lhs mouse button <=. Within this window the "user interface" follows the same guidelines as a Macintosh computer. Text can be selected, copied to a "clipboard", cut or pasted and to help you do this, "pull-down" menus can be invoked by locating the mouse over them. In the File menu, files can be opened, saved etc. Most importantly, be aware that anything you type in this window will have to be saved before it can be used by another program such as a compiler. When saving a file, you have to inform the operating system in which directory the file will reside. You should adopt the working practice of saving the file every few minutes or so in case a computer crash occurs and you lose all your work. Save should also be invoked before attempting to compile the program. The Edit menu contains the usual options for manipulating text and Search has text locating utilities. Finally Help is similar to the ballon help item on a Macintosh.

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Manual Pages.

If you want help on any Unix style command, the Manual pages can be invoked;

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New Window

This creates a new console like command line window. It differs from the Login window in being associated specifically with the workstation you are using, and from the Console window in not being the recipient of system error and informative messages. As many windows as you can cope with can be so created. The reason for doing this is you may wish to reserve one window for say compiling a program, a second specifically for running it, and a third perhaps to check disk space usage and other book-keeping tasks.
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Fairly self-explanatory. Never switch the workstation base unit. Sometimes a program called "Window manager" can crash, resulting in your workstation screen "freezing up", making it impossible to log-out. The best advice is to simply leave it in this state. It does not represent a security hazard, since only the system manager can clear this state. off.
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Sometimes, so many windows can be open simultaneously that it is easy to get lost. The windows menu offers several options for finding ones way around lost windows. Perhaps the most useful is Minimise all, which reduces all the windows to something that looks like this;

From here, click on the window that you do want to open it up.
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Electronic Mail.

Ywo programs for reading e-mail are available. By default, the Toolchest invokes "elm". Some people prefer another called "Pine". These are excellent for sending simple text based messages. Another method of sending (but not receiving) e-mail is to use the so-called "mailto:blogs@somewhere" URL in the Netscape browser. If you are reading this in Netscape, try clicking on the above hyperlink to see how it works. If you want to "attach" a document with your e-mail you should use Eudora available on the Macintosh systems. If you want to send a message, you will automatically enter the text editor described above in order to compose your message.

Warning about disk space: Most e-mail messages "date" fairly quickly. You should get into the habit of deleting old messages, and also saving the particularly important ones elsewhere. It is surprising how much disk storage space e-mail messages can occupy. If your mailbox is occupying significant amounts of space (> 1 Mbyte), it may be unilaterally (and unselectively) purged for you!

Mail Lists

There are many so called subscription e-mail lists on the Internet. It is very simnple to join these, but once you do, you run the risk of receiving large amounts of unsolicited e-mail. Some e-mail lists even post weekly newsletters in Postscript form which can each be 200-300k in size. Unfortunately, whilst people find it easy to join lists, they somehow never seem to bother to leave them. The consequence is that a large number of e-mail messages continue to be received by registered users in the department, sometimes after they have graduated and left. There is no restriction on joining subscription lists, provided you delete messages after you have read them.. If this is not done, you run the risk of having your account invalidated.

Warning about misuse of E-mail: You are reminded that your e-mail account is a privilege which should not be used to bring yourself, the department or the College into disrepute. In particular, using e-mail in an offensive manner, or transmitting inappropriate pictures could result in disciplinary action. If you are unsure where you stand on these matters, consult the formal notice which should be pinned to the computer rooms.

Click here for further details of e-mail

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Plotting and Printing.

Unlike a Macintosh, all printing is achieved by writing out a plot file to disk and then using a "post-processor" to send it to a plotter. You have three options at this point.
  1. SYBYL, MacroModel, Quest and other programs have Plot or Print options, which when invoked request the name and possibly type of plot file you wish to save. Normally this will be a "Postscript" file which can be sent for printing in the following way; Enter a console or shell window and type;
    iron$ deskplot bloggs.ps
    iron$ deskq (for information on the state of the queue) The output will appear on the HP Deskjet in room 337. Since colour printing is very expensive, you must not generate more than 1-2 plots. If you want to do a lot of colour printing, you will be asked to provide your own colour ink cartridge. There are also some high quality colour postscript printers which can be used, but only in consultation with Henry Rzepa.
  2. You can create a screen "snapshot" of any portion of the screen and save this as a "rgb" file. To do this, type at a prompt;
    and place the small rectangular outline somewhere which will not obscure your desired image. Place the mouse cursor over the snapshot icon, and press the lhs button once. Next, press the shift key, and keeping it pressed, move the cursor to the top left hand side of the image you want to capture. Press the lhs button and "drag" the outline that appears to the bottom right hand side of the capture area. Release the lhs button. Now return to the shapshot icon, activate it with the lhs button, and then press the rhs mouse button. A menu appears, the top item of which will perform the image capture. The file by default is given the name snap.rgb and can be processed as described below. You can also change its name within the same menu. Explorer also produces such rgb files from its own internal "snapshot" module. Such files can be printed using a different utility which first converts the rgb file to postscript, adds a header so that you can identify your own output and then sends it to the printer. To invoke this mode type;
    iron$ugplot bloggs.rgb
    (note that the .rgb qualifier must be present).
  3. Both .ps postscript files and .rgb files can be transferred to a Macintosh computer and processed there. A .rgb file must first be converted in the following way;
    iron$tp bloggs
    This produces a file called bloggs.pict, which is now transferred to a Mac using the Fetch program (remember to set the file type to binary and the file type to PICT) in the Fetch menus that appear). The file can then be opened using Teachtext, or other word processors or graphics programs. All the "snapshots" in this document were processed in this way.

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If the workstation is not responding correctly, or at all, you should report the problem to Sue Johnson (4567) or Henry Rzepa (45774), quoting the name of the system. This is indicated on the little blue sticker on the screen. Each system is named after an element to help you remember! If it looks likely that you will be the last user at night, the monitor can be safely switched off to conserve electricity. DO NOT however power the system unit in the indigo coloured box.
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Copyright (c) H. S. Rzepa and ICSTM Chemistry Department, 1994,1995.