A. Le Bail, Laboratoire des Fluorures, URA CNRS 449,
Université du Maine, 72017 Le Mans, France.
A Conference Presented at The XVII Congress and General
Assembly of the International Union of Crystallography, Seattle, USA, August
8-17, 1996 (see also the VRML
page corresponding to the Workshop Surfing the Crystallographic
Exploring a crystal structure from the inside and really understanding it: the Virtual Reality Modelling Language (1) allows this and much more. Simple applications can readily be produced without specialist knowledge. Use your favourite drawing program, decide what you would like to see (select atoms), convert your data into a standard .wrl file and then view the result on almost any platform. A PDB (Protein Data Bank) to VRML converter already exists (2).The whole operation (apart from PDB2VRML which is UNIX only) can even be carried out on just a fast PC although graphics workstations improve productivity. For inorganic structures an excellent procedure is to convert SHELX .ins into .pdb files using BABEL (3), select those atoms suitable for the display required, verify the result with RASMOL (4) and finally create automatically the .wrl file with PDB2VRML. A change in the pre-defined radius and colors can be undertaken by editing the ASCII .wrl file. A more direct builder is xtal-3d (5) for UNIX platforms, a PC adaptation being planned.
The most exciting moment during the course of a crystal structure determination occurs when enough atomic positions are known to be able to draw at least a partial model. The less exciting is when it is realized that the structure is so complex that it will be necessary to build a real 3D paper (or ball and stick) model in order to be sure that nothing has been overlooked in the structure description. VRML can help one to do almost the whole job in a few minutes starting from standard drawing files. Visual applications are limited only by ones own imagination. For the specialist it is feasible to create 3D crystallographic scenarios, calling objects stored at different URLs on the net. The real usefulness to crystallography of 3D mark-up is an open question.
1. J.C. Hardenbergh, http://www.oki.com/vrml/VRML_FAQ.html
2. H.Vollhardt, http://ws05.pc.chemie.th-darmstadt.de/vrml/pdb2vrml.html
3. P. Walters & M. Stahl, http://mercury.aichem.arizona.edu/babel.html
4. R. Sayle, ftp://ftp.dcs.ed.ac.uk/pub/rasmol
5. M. Hewat, http://188.8.131.52/dif/3D_crystals.html
Slide 1 - Examining three-dimensional models in crystallography is as old as crystallography itself. Models were built by hand in paper, wood, metal and then plastic. Three-dimensional graphics on computer is quite old too. At the beginning of the eighties, powerful dedicated computers were yet able to show and allowed you to rotate models of considerable size. Moreover, none of the models built up to now in crystallography show the reality, all are virtual. So, what is new ?
Slide 2 - The World Wide Web is new, and it is time to select a standard language for description of three-dimensional objects which could be shared on the net and visualized on any platform. Only two years ago the basis for the Virtual Reality Modeling language were built from Silicon Graphics Open Inventor language. It is not a computer language but an intuitive tool for scene description by text. Common objects like cubes, cylinders or spheres are simply called by their names. The opportunity to adopt this language for describing crystallographic objects should not be missed. This is what I want to argue for.
Slide 3 - The best is to begin with a simple example : how to make appear two spheres on your computer screen. A VRML file is a text file. After a first line of comment defining the VRML version are defined the scene elements (nodes). Here the background color is defined by its Red, Green, Blue components giving white. The first sphere is at Cartesian coordinates 0/0/0 by default and the second one is translated by 1/1/1 both are colored in blue lagoon. If you click on the first sphere, you will load and display another VRML file stored at the Institute Laue Langevin. VRML example 1.
Slide 4 - A software called Viewer is required in order to render a VRML file on your computer screen. A Browser is the program which reads the VRML file on the Web. Some software do both actions, some Viewers may run as standalone applications or plugged-in Browsers, some allow authoring. More than 30 such softwares are available, most of them are FREEWARES. Note that graphics shown in this conference were prepared by using Netscape 3 and Live 3D.
Slide 5 - Most of these Browsers or Viewers are multiplatform. A point I would like to insist on is that almost all graphics shown here were realized on a PC Pentium 100MHz. This will be the reference machine for defining what is possible and what is not. If you are more fortunate than me, you might be able to do really much better ! The Moore principle will allow everybody to do much better soon and PCs three time faster than mine yet exist.
Slide 6 - We return now to the trivial example. You have seen two spheres with a smooth rendering. Some Viewers allow to play with rendering. Here is selected a flat shading rendering where it is apparent that spheres are built from polygons (nearly 100). Selecting wireframe shows the polygons boundaries. VRML example 1 : select flat shading, then wireframe.
Slide 7 - Because it was defined for the Web, VRML has full markup capabilities. That is to say, all elements of the 3D scene may be linked to any file in the whole Web. Either another 3D file or a Web hypertext page or a sound, a picture, a movie... you can jump to them by a simple click of the mouse. This is useful for writing interactive tutorials or showing a Chemico-crystallographico-scenario. This example is again from the Alan Hewat Collection and illustrate BCC. The VRML text file corresponding to the scene is shown at the bottom. VRML example 2 : find the sphere with a markup and click.
Slide 8 - If you possess the biggest graphics workstation, there is almost no limitation apart your imagination for the use of VRML. If you work with a Personal Computer you may have deception sometimes. The complexity of objects you can manipulate with the reference micro-computer chosen here, a low end Pentium, is 10000 polygons. This means 100 spheres or nearly 2500 tetrahedra if they are represented by faces or 10000 atoms with a wireframe rendering. On another hand, crystallographers want to be able to save high quality 2D views for eventual publication. You may obtain acceptable results by screen copy at high resolution for the moment.
Slide 9 - Taking an example from Darmstadt, here is a ball-and-stick model of an enzyme active site. With nearly 50 spheres and cylinders, such an example can be manipulated very fast on the Pentium reference micro-computer. Now, if you try to see the whole enzyme as ball-and-stick, you can't. The model is too big. However it would be possible to see it as wireframe. VRML example 3.
Slide 10 - The complexity limit as wireframe on the Pentium 100 is comfortable as you can see for a model taken from the Imperial College, London. This helicoidal graphite model presents 2000 atoms and equivalent graphics quality and movability are obtained from either VRML and a Viewer or the original PDB file combined with the well known RASMOL software. VRML example 4 and corresponding pdb file to be seen with RASMOL.
Slide 11 - Now, if we try to see the graphite model as ball and stick by VRML on the Pentium 100, this is impossible. You will have now a possible explanation why people working on large molecules dislike VRML for the moment and prefer to use a software like RASMOL which has been even ported as the graphics engine into Chemscape, a plug-in for the Netscape Browser. With RASMOL, you can even rotate the 2000 atoms as ball-and-stick on the Pentium 100. You could too with VRML installing 32Meg RAM instead of 16 on the PC or with almost any Silicon Graphics workstation. WARNING, the VRML example 5 is big and may overload your computer. Compare with the pdb file seen as ball-and-stick with RASMOL.
Slide 12 - If VRML becomes the standard for 3D in electronic publication, then no doubt that all commercial structure drawing software will propose a VRML output option soon. For the moment one can find two kinds of authoring tools, software dowloadable on Internet or builders on-line. All will not be shown here but a selection of seven of them in alphabetical order.
Slide 13 - Builder 1.2 is dedicated to membranes. Once connected you fill in the form specifying how many of each solute you want to have in your membrane. Then you get the VRML file in return on your screen. Of course you have the possibility to save the VRML text file on your hard disk to see it without being connected on the WEB. Such membranes were too big for my small PC so I have selected only a lipid molecule to show you from this site. VRML example 6.
Slide 14 - CRYSTAL is a program to make ball-and-stick or polyhedral crystal structure drawings. The source is available in C language. Here are some example of VRML files built with it. The Web site is dedicated mainly to silicates. Those making themselves their structure drawings for publication know that to be happy with the result you have to work generally several hours. VRML does not change that of course. You must think to what you want to show. However, being able to walk inside the model is of great help for decision. VRML example 7.
Slide 15 - The next example is a Japanese database of crystal structures (JICST) among which you have to choose which one you want to see. The choice of the rendering as ball-and-stick, stick or space fill is also yours. The inconvenient is that you cannot draw your own new structure. VRML example 8.
Slide 16 - MOLDA is an interactive molecular and graphics system working on Microsoft Windows 95 or NT accepting various file formats including MSC's Xmol XYZ. Drawings may be seen using MOLDA itself or by a VRML Viewer after having saved your work as a VRML file. You have the choice between three possibilities of rendering : dreiding sticks, ball and stick and space filling. VRML example 9.
Slide 17 - PDB2VRML from Darmstadt is online or downloadable in executable form for various UNIX platforms. So you can't use it on your PC unless your operating system is LINUX. However since you are connected, do not move from your desk and connect by TELNET to a distant UNIX machine on which you have installed the pdb2vrml software as shown in the upper box. The program runs with a simple command line. The PDB file is converted into VRML choosing between various rendering possibilities. Although the program is focused on protein structures, you may apply it to inorganic structures too, this is the case for the example shown. VRML example 10.
Slide 18 - STRUVIR is a program more specifically dedicated to inorganic structures with a polyhedral rendering. It has been retained for distribution in the CCP14 suite and will be available soon for a large variety of platforms as freeware for academics. WARNING : the VRML example 11 is really big.
Slide 19 - XTAL-3D can be used either at home after downloading the software or on-line by pasting your atom coordinates into the form loaded at the ILL Alan Hewat Web site. Probably this software will be retained by the Inorganic Crystal Structure Databank for displaying 3D structures on Internet. VRML example 12.
Slide 20 - VRML is so young that one cannot be sure it will still exist in a few years. One can observe a 100% increase in VRML activity during the last 5 months. A lot of companies and individuals have interest in VRML duration but who knows ?
Slide 21 - Not only you can rotate and translate VRML worlds, but objects can seem alive and move in a way predefined by the VRML writer. Here are two examples with a woman throwing a boomerang or a dancing ballerina. VRML examples 13 and 14.
Slide 22 - In conclusions, 3D is really exploding on the Web and crystallography applications are probably not even 1%. The main interests are : 3D at low cost for personal use, teaching and electronic publication.
Slide 23 - This final view is for those for which a virtual coffee is sufficient. Not my case. VRML example 15 : go inside and find the cafe, be curious and look on the tables.
Slide 24 - Finally, here is a last minute announce for the commercial software CRYSTALLOGRAPHICA from Oxford-Cryosystems in which an option for saving structures in VRML has just been added. VRML examples 16, 17, 18, 19.
hope this help
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