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Tutorials and Examples

ORTEX for Windows Single Crystal Suite by Patrick McArdle

Creating a photorealistically rendered movie of a packed cell

The CCP14 Homepage is at http://www.ccp14.ac.uk

[Tutorials page] | [ORTEX Tutorial Index]

The latest ORTEX (April 2001) can take any Shelx file and create a rendered GIF animation of a packed cell with relatively simple ease.

The main strategy is to run ORTEX, enter the pack range. Exit ORTEX, use LISTU, then re-enter ORTEX and exclude any offending fragments; then exit ORTEX and run RASMOV.

The following uses the Tetracycline Hydrochloride structure as an example.

In the ORTEX directory, run Oscail to bring up the following starting Window

Oscail Starting Screen

Click on the J (Job name) Icon and change the name of the jobname to tetcy. If not in the \ortex directory where the tetcy.ins file is located, click on the change directory icon and enter this directory. (in this case in the \ortex\tetcy directory)

Changing the Job Name

Before you can render the movie, you must obtain the view of the structure that you wish to render by running ORTEX.

Thus select the Run Job Icon which brings up the main control menu in the ORTEX Suite.

Run Job Menu

Select ORTEX and press OK to bring up the ORTEX graphics. If queried, select defaults

Ortex Graphics

Select the top left Start ATOM Mode Icon

In Start ATOM Mode

Select the Lattic Pack Icon and Lattice Pack options.

Lattice Pack Options

Lattice Pack Options

The idea is to include more molecules than you need and trim them back. Select Auto and enter a pack range that goes slightly beyond the range of molecules you wish to animate. In this case 0 to 1.5 on all axes. Then click on the Stick Mode and then exit ORTEX to be sent back to the main menu.

Lattice Pack Options

Generated structure

Now select the use LISTU menu option (this now allows you to delete fragments with associated AFIX and other Shelx commands) and then re-enter ORTEX. Then select the Start STICK Mode icon (2nd from the top left)


Packed structure in Stick Mode

To delete a fragment: select an atom on the offending fragment to be deleted, then the DEL.Frg menu option; and save changes to the INS file. Repeat going into Stick Mode until you are happy with the trimmed down lattice pack. You may be left with something like the following.

Now Exit ORTEX back to the main menu.


Select the Start RASMOV Movie Generator Icon to start on the way to generating the movie.

(If the RASMOV Movie Generator detects that you have a cell packed structure, it will prompt whether you wish to use this "ORTEX" generated file. Respond with the affirmative if you wish to use the cell packed structure)

In the Start RASMOV Movie Generator menu

Select the options that appeal to you. In this case, a 384 x 320 pixel movie, with shadows, and 360 degrees range at 5 degree steps with no oscillate. Make sure the lock mode is on if you do not want the molecule dynamically resizing to fill up the entire screen.

Setting RASMOV Movie Generator options

Press OK and the GIF movie file will be rendered. At the end, it will prompt whether you wish to use the TIF, GIF and R3D files used to generate the movie. Unless you wish to make use of some of these files, YES might be a good answer.

You can then choose how you wish to view the GIF animation (the default is in your default web-browser)

Prompting to delete excess files and view the GIF animation

If the image does not come out as expected, go back into ORTEX and modify until the desired results are obtained.

To view the movie, click on the following. (1.4 Meg GIF Animation). Again, if the animation is not good enough, try again to get the effect you desire.

Tetracycline Animation Produced by the Ortex Suite - 1.4 Meg

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