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C I N E C H E M Molecular Rendering and Animation with HyperChem and 3D Studio --- with --- S T I N G R A Y Stingy Ray Tracer by John Walker Release 0.3 -- 13th October 1992 INTRODUCTION ============ HyperChem allows you to build molecules, analyse them in various ways, and perform simulations of molecular dynamics. HyperChem also includes a variety of rendering algorithms including stick, dot surface, disc, and space filling sphere representations of molecular structures. While these renderings are entirely adequate for grasping the conformation of a molecule, they are not comparable to those created by high-end systems. In addition to rendering still image of molecules, HyperChem's ability to save "Snapshots" in the course of a molecular dynamics simulation enables one to create animations of dynamics runs: the "molecule movies" which many think are achievable only with supercomputers. While more comprehensive rendering and animation support could be added to HyperChem (and undoubtedly will be as the product matures), Autodesk already sells a product which contains everything needed to create high-end molecular images and animations: 3D Studio. Unfortunately, HyperChem and 3D Studio models are entirely incompatible, preventing the user from harnessing these two complementary products into an integrated scientific modeling and presentation tool. CINECHEM bridges the gap between HyperChem and 3D Studio. Simple and easy to use because it relies on the existing user interfaces of HyperChem and 3D Studio rather than providing its own, CINECHEM permits the HyperChem user to create renderings an animations within an hour of installing CINECHEM and 3D Studio on his machine. JUMP START ========== 1. Install It -------------- Copy the contents of the CINECHEM release disc into the directory in which you keep your HyperChem model (.HIN) files. 2. Make a Rendering -------------------- Fire up HyperChem under Windows, open the system you'd like to render, and establish the viewing position for the picture using HyperChem's pan, rotate, and zoom tools. When you're happy with the viewpoint, save the system in .HIN format. (If you already have one or more .HIN files, you don't need to edit them with HyperChem, naturally). Try a reasonably simple molecule the first time so things don't take too long. After saving the .HIN file, exit HyperChem and quit Windows. (3D Studio is a non-DPMI-compliant 386 mode application, and it cannot run in a Windows DOS box. CINECHEM, however, will run under Windows.) Once you're back at the DOS prompt, run CINECHEM on the .HIN file: CINECHEM <name>.HIN If you omit the ".HIN", CINECHEM will supply it for you. When CINECHEM is done, you'll have a <name>.3DS file in the same directory as the .HIN file from which it was created. Load 3D Studio, and using "Load" on the "File" menu, navigate to your <name>.3DS file and load it. You'll see a variety of viewpoints on the screen. Click the mouse in one of these viewpoints and type "C" to supplant it with the "Camera" viewpoint. Then, using the menu at the right, select "Renderer", then "Render", then click in the Camera viewpoint to designate it as the viewpoint to be generated, then click "Render" once again for spirit at the huge and confusing dialogue box that appears. Clinkity, clankity, clunk, and in a few seconds (or more, if your machine is pokey), there's your picture! This initial rendering is, of course, just the point of departure for creating publication quality art; all of the facilities of 3D Studio are now at your disposal, so you can change material types, lighting, viewpoints, perspective, etc., without recourse to HyperChem or CINECHEM again. (Note that this means a HyperChem user can turn over "raw molecules" processed by CINECHEM to a 3D Studio expert for rendering, instead of becoming a 3D Studio expert himself.) 3. Make an Animation --------------------- To make animations, we assume you already know how to run a molecular dynamics simulation in HyperChem. If you don't and wish to learn, please refer to Chapter 10 of the HyperChem "Getting Started" manual, paying particular attention to section "Setting up Playback Dynamics" on page 147. Run your simulation with Snapshots enabled, saving the results of the simulation in a <run>.HIN and <run>.SNP file. (Normally, you'll save the simulation snapshots with a different name than your original .HIN file). Animations generally look best if you set the Snapshot period to 1 data step, although if you're using a very small time step you may wish to increase the snapshot period to reduce the size of the animation and the time required to generate it. To create a 3D Studio animation of the simulation, you need only invoke CINECHEM on the .SNP file: CINECHEM <run>.SNP CINECHEM assumes that <run>.HIN is in the same directory as the .SNP file and will error if it cannot be found there. If you omit the ".SNP", CINECHEM will search first for a snapshot file to animate and, if none is found, then look for a .HIN file to create a still image. As before, the results of CINECHEM will be found in a <run>.3DS file in the same directory as the .SNP and .HIN files. Exit HyperChem and Windows, fire up 3DS, and load the file as for the still rendering before. Don't panic---when the image appears on the screen it may look very odd; what you're seeing is the base model, not the actual frames of the animation. Select the Keyframer on the Program menu (or just hit F4), and you'll see the first frame of the actual animation. You can move the slider along the bottom of the screen to preview the motion of the atoms and bonds over the course of the simulation. As before, click in a viewport and type C to change it to the camera viewport, select Renderer, then Setup and configure the screen resolution you desire. Next select Render, click in the Camera viewport, enable "Disk" in the dialogue box to save the animation in a file, and click Render. The animation will be created and saved in an .FLC or .FLI file according to the resolution you requested. You may then play the animation within 3D Studio (assuming you have a suitable VGA-compatible display), or with the public domain AAPLAY or ANIPLAY utilities furnished with Autodesk Animator and Animator Pro. VARIETIES OF THE RENDERING EXPERIENCE ===================================== You can control the operation of CINECHEM through specifications on the command line (file names and options) and through an optional configuration file which allows you to assign 3D Studio material types to various elements and bonds. The general form of the CINECHEM command line is: CINECHEM [options] infile[.HIN/.SNP] [outfile[.3DS/.NFF/.POV/.RIB]] If no [outfile] is specified, <infile>.3DS is assumed. If <outfile> is specified but no file type is given, ".3DS" is appended. If no file type is given for <infile> CINECHEM searches first for a .SNP file and the corresponding .HIN file from a molecular dynamics animation then, if no .SNP file is found, for an .HIN file to be rendered into a still image. CINECHEM accepts the following options: -A Set screen aspect ratio. (NFF/POV/RIB) -B Do not display bonds. -C<file> Load the named configuration file. If no file type is supplied, ".CFG" is assumed. (3DS) -D Dry: water molecules are not rendered. -E<factor> Expand (or contract) the distances between atoms by the given <factor>. This gives you smooth control over the relative size of the atom spheres and the bond lengths. The "-S" option is equivalent to a specification of "-E3". -H Do not display hydrogen atoms or bonds to them. -K Generate keyframer hierarchy to make atoms and bonds child objects of the molecule that contains them even if the input is a static model (.HIN) file instead of a model/snapshot (.HIN/.SNP) pair. This is handy when you want to manually animate a model to show, for example, how a molecule binds to an active site of another or to create animations of so-called "nanomachines". (3DS) -M Create special material types for each element and bond used in the model. (3DS) -Q Quiet (suppress sign-on line). -R<n> Rendering quality versus time tradeoff. If <n> if 0, rendering will be very fast but picture quality will be low. As <n> increases toward the maximum value of 9, image quality improves at the expense of rendering time. The default value is 7. (RIB) -S Generate a "stick and ball" rendering rather than the usual "space filling" representation. The spheres that represent atoms are reduced in size by a factor of three so they appear as balls at the junction of sticks representing the bonds. -T<factor> Thicken the bonds by the specified <factor>. A <factor> of 1 yields the default thickness, 2 twice that thickness, and 0.5 half the default. This is primarily intended to make bonds more visible when rendering stick and ball pictures for low resolution displays. -U Display a summary of the command line and options. -X<pixels> Set screen width to <pixels>. (NFF/POV/RIB) -Y<pixels> Set screen height to <pixels>. (NFF/POV/RIB) Some options are applicable only to certain output file formats; they are noted in the table above. Options irrelevant to the current file format are ignored. SPECIFICATIONS IN THE MATERIAL WORLD ==================================== By default, CINECHEM chooses 3D Studio materials which reproduce the default colours that HyperChem uses when rendering atoms. (Note that if you change HyperChem's rendering colours with the "Display / Element Color..." dialogue, CINECHEM does not automatically use those new colour assignments. Bonds are rendered according to the type of the bond as follows: Bond type Material --------- --------------- Single White plastic Double Blue plastic 50 Triple Copper Aromatic Gold You can change these material assignments by supplying a configuration file which assigns specific 3D Studio materials, either from the standard library or those you've created yourself, to elements and bonds. Here's a sample configuration file: ; Gaudy show-off configuration element_3ds H tile goldgranite element_3ds o red glass element_3ds c blue planet element_3ds n blue metalic element_3ds s yellow plastic element_3ds lp marble - pale bond_3ds s blue marble bond_3ds d ape bond_3ds t blue plastic bond_3ds a old metal Upper and lower case letters are treated as identical in processing the configuration file, blank lines are ignored, and any text on a line following a semicolon is taken as a comment. Two statements may be supplied in the configuration file: ELEMENT_3DS <element_symbol> <material name> This assigns <material name> (which may be any number of words) to the element with chemical symbol <element_symbol>. The <material name> must be defined in one of the libraries from which 3D Studio obtains material definitions. You can assign a material to lone pairs by using an element symbol of "LP". BOND_3DS [S|D|T|A] <material name> Assigns <material name> to the bond type (Single, Double, Triple, Aromatic) specified. The <material name> must be defined in one of the libraries from which 3D Studio obtains material definitions. A configuration file can be specified by naming it with the "-C" option on the CINECHEM command line, for example: CINECHEM -Cgaudy MYDNA.HIN where GAUDY.CFG is the configuration file that specifies rendering for MYDNA.HIN into MYDNA.3DS. Any elements or bond types not specified in the configuration file will be rendered according to the defaults. If no "-C" specification is given, CINECHEM will look for a configuration file named CINECHEM.CFG in the current directory and, if present, load it. An alternative method of managing material types is provided by the "-M" option. If you specify this switch, a material will be created for each type of element and bond which appears in the model. These material types are given names like: Hydrogen atom Carbon atom Neodymium atom Single bond Double bond Triple bond Aromatic bond ...etc. The materials are initialised to render in the default colours described above (if the "-M" option is selected, the configuration file is ignored). Choosing the "-M" option creates a 3D Studio model in which it's easy to change the appearance of specific kinds of atoms and bonds; just go to the Material editor, get the material you wish to change from the scene, modify it as you like, then put it back to the scene and re-render. You can use the "-M" option in conjunction with libraries which define materials for various elements and bonds, as well. RENDER UNTO OTHERS ================== By specifying an output file with an explicit extension, you can cause CINECHEM to create an input file for any of the following renderers: Extension Renderer --------- -------- .3DS 3D Studio (default) .NFF StingRay .RIB Autodesk RenderMan .POV Persistence of Vision Raytracer None of the other renderers support animation, so even if you supply a snapshot file from a molecular dynamics simulation, only a rendering of the initial image will be created. The material specifications in configuration files and the optional assignment of material names based on element and bond types affect only 3D Studio output files. For example, to render a system called MYDNA.HIN into a Microsoft Windows bitmap file with a resolution of 640x480 pixels using StingRay, use the commands: CINECHEM mydna mydna.nff -x640 -y480 STINGRAY mydna You can then view the resulting MYDNA.BMP file with your favourite Windows bitmap display program. StingRay -------- StingRay (STINGy RAY tracer) is a public domain raytracer included with CINECHEM. It allows users to get started in high-quality molecular modeling rendering under Windows without the need to purchase 3D Studio. For some applications (particularly those where reflection and refraction are important, or where precise rendering of sphere and cylinder contours are important, as opposed to polygonal mesh approximations) it produces superior results. Since StingRay is a batch renderer with no user interface (or even display support), customising the pictures it generates requiring editing the model (.NFF) file with a text editor; this is obviously a lot less friendly than 3D Studio, but experts can create very classy images that way. Autodesk RenderMan ------------------ Autodesk RenderMan is Autodesk's licensed version of Pixar's renderer which implements the portable RenderMan scene description language. AutoShade users who possess a copy of Autodesk RenderMan can use that renderer on HyperChem models by specifying an extension of ".rib" on the CINECHEM output file. The ".rib" file written by CINECHEM will be configured to render with very high image quality (and correspondingly slow rendering speed), with the image size, width, and aspect ratio given by options on the CINECHEM command line (defaults are a 640x480 pixel image of square pixels). Output is written to a Truevision Targa (.TGA) file with the same name as the input .RIB file. You can change all of these parameters by editing the .RIB file before processing it with RenderMan. Persistence of Vision Raytracer ------------------------------- The Persistence of Vision raytracer is a descendent of the DKB raytracer developed by David K. Buck. It was subsequently extended by a team of volunteers on CompuServe led by Drew Wells. POVRAY is a thoroughly professional, high-end rendering engine which implements primitives and provides capabilities absent from many expensive commercial products. Surfaces and solids up to quartics are supported, along with deformable "blobs", texture and bump mapping, and CSG operators. The Persistence of Vision raytracer is essentially in the public domain, but there are restrictions on its commercial dissemination which preclude supplying it with CINECHEM. You can obtain a current copy of POVRAY (including source code) from the COMART forum on CompuServe. POVRAY usually lives in Data Library 16, but check the "recent uploads" sections since CompuServe "saves space" by not duplicating the latest updates into the sections in which they will eventually reside. WHAT IS THIS "STINGRAY", ANYHOW? ================================ 3D Studio combines a powerful collection of rendering facilities with an unparalleled user interface to animation which makes it the product of choice for high-end presentations; the awards it has won and the work produced with it demonstrate this. But 3D Studio has one major drawback; it's *expensive*. Chemists are poor. It's very hard to justify a US$3500 out of pocket expense to produce pictures that spice up one's publications. But if people could just get a taste of high-end rendering, then they'd want *more and more* and eventually be satisfied with nothing less than the Real Thing, including animation. Enter StingRay. StingRay stands for "STINGy RAY tracer"; it's a slightly extended implementation of the "MTV Raytracer" originally implemented by Mark VandeWettering, then of the University of Oregon. The author released this ray tracer into the public domain totally free of restrictions: This program is public domain. Feel free to modify it, hack it, use it inside other programs, and even sell it. I wrote it to better understand raytracing and hope that it helps others understand the raytracing process as well. StingRay is stingy in that it's free to acquire (including source code), but it's rich in functionality; in fact, it provides most of the facilities found in top-of-the-line molecular rendering systems. Its shortcomings are mostly in the representation of complex geometry which isn't used in molecular modeling, and in fancy optimisations to speed up the rendering process. The quality of the the images created is entirely comparable to those created by commercial products. StingRay is called with a command of the form: STINGRAY [options] input[.nff] [output[.bmp/.tga]] The input file is assumed to be a scene description in a slightly extended version of Eric Haines' Neutral File Format (NFF). The only extension supported by STINGRAY is a new "aspect" statement which permits specification of pixel aspect ratio for non-square screens. StingRay creates output image files in either Microsoft Windows Bitmap (DIB) format (.BMP files) or in TrueVision Targa-24 (.TGA) format. The format of the output file depends on the extension given on the output file name. If no output file name is specified, the output file will be written in Microsoft Windows bitmap format to the file <input>.BMP. StingRay always creates a full colour image (24 bits per pixel). If your display does not support full colour images (or a subset thereof, such as the 16 bit per pixel "high colour" displays), be sure to use an image viewing program that intelligently compresses the full colour image into one compatible with your display. If you just view the bitmap on your 256 colour display with Microsoft Paintbrush or WinGIF, you'll be disappointed since the true colour image will be brutally crushed into the Windows default colour palette. To do justice to the image, you need to intelligently flatten it to a custom-generated 256 colour gamut. You can do this with the ANICONV utility supplied with Autodesk Animator PRO, with the public domain PICLAB program available on CompuServe or, if you're a Unix user, with the PBMPLUS utilities. If the utility you're using doesn't read .BMP files, you can create a Targa (.TGA) file by executing StingRay as follows: STINGRAY mydna mydna.tga ANICONV, PICLAB, and PBMPLUS all process full colour Targa files without difficulty. A copy of the current release of PICLAB is included with CINECHEM; it is also unrestricted public domain software. You can control the rendering process by specifying options on the STINGRAY command line: -Aratio Set screen aspect <ratio> -F Fast and cheap antialiasing -Josamp Antialias by oversampling <osamp> times -Q Quiet (no sign-on line) -T Show progress by line number -U / -? Print this message -V Verbose: print model and timing statistics -Xpixels Set screen width to <pixels> -Ypixels Set screen height to <pixels> Normally, the image size and aspect ratio are specified in the .NFF file that defines the model to be rendered; you may override these values with the "-A, -X, and -Y" options. The first time you run StingRay you may be disappointed with the results; you may notice "jaggies" and other rough edges that don't look like high-quality contemporary renderings. There's an unavoidable tradeoff between image quality and rendering time, and StingRay implements this in a very brutal fashion: N squared time. The "-Jn" switch, which enables stochastic oversampling of subpixels, controls the tradeoff between speed and quality. If you specify "-J16", each pixel of the final image will be the average of 16 randomly positioned subpixels within the box bounding the pixel in image space. The resulting image will be *beautiful*, but it will take *sixteen times* as long to create as a simple image with no oversampling. More sophisticated renderers, including POVRAY, use an adaptive oversampling algorithm which only calculates additional rays after detecting a sharp edge in the image; StingRay admits of no such sophistication. It's slower, but the image quality is impeccable. As an alternative to exhaustive oversampling with the "-Jn" switch, you can select quick and dirty smoothing with the "-F" switch; this simply averages groups of four pixels. This takes the bite off rough edges at the cost of a subtle blur to the overall image. HARDWARE AND SYSTEM REQUIREMENTS ================================ CINECHEM and StingRay are intended to be used by HyperChem customers on the same machines on which they run HyperChem. Both were produced with WATCOM C 9.0 and a PharLap DOS Extender which is fully DMPI-compliant and runs either under a raw DOS environment or within a DOS window in Windows 3.1. If you're running HyperChem on your machine under Windows 3.1, you should have no trouble running either CINECHEM or StingRay in a DOS window. (Note that this permits you to save a model from HyperChem, process it with CINECHEM, render it in the background with StingRay, and view the results with a BMP display program, all without ever leaving Windows.) CINECHEM's memory requirements vary based upon the number of atoms in the model being generated and, for an animation, the number of snapshots to be rendered. In most cases, one or two megabytes are plenty. Lengthy animations of huge molecules can require lots of memory, but you'll probably run out of patience or disc space before RAM is exhausted. StingRay is as conservative in its memory usage as it is profligate in consuming CPU cycles. Essentially, only the model is kept in memory (unlike renderers which require enormous "reflection maps" and/or "shadow maps"), so one or two megabytes should suffice for huge molecules and high resolutions. StingRay requires a math coprocessor, but CINECHEM doesn't--it's not sufficiently compute bound that it would benefit from the restriction. Neither program benefits from a Weitek chip, if present. DETAILS AND DE BUGS =================== CINECHEM attempts to create 3D Studio camera and light objects which reproduce the same view of the molecule in 3D Studio that HyperChem displays when viewing the same .HIN file. Unfortunately, HyperChem doesn't indicate if a perspective view was enabled. CINECHEM always creates a perspective view (except when generating a RenderMan file), because all the renderers other than RenderMan work exclusively in perspective. Since HyperChem usually places the default camera far away from the molecule, perspective effects are not normally very great, but in some cases you'll want to adjust the camera's field of view to fill the frame with the molecule, taking account of perspective. The version of 3DSLIB used to build CINECHEM doesn't allow specification of an arbitrary viewport configuration. You're either stuck with the 3D Studio default configuration or one full-screen viewport to your specifications. Rather than fill the screen with the camera viewport (from which you can't adjust the camera and light locations), I opted for the default configuration which requires you to type "C" in a viewport to see the image to be rendered, but avoids endless fussing if you want to adjust the camera or light. If the "-M" option is not specified, CINECHEM has no need to place material definitions in the .3DS file it creates--it's relying exclusively on materials already defined in libraries accessed by 3D Studio. Nonetheless, CINECHEM defines a material called "Void of space", which it never actually assigns to an object. Why? Because if it doesn't, when you load the .3DS file, 3D Studio issues the jerk alert: CAUTION: File contains antiquated data type, please re-save which is as annoying as it is grammatically wrong (comma-splice), but if and when somebody provides me a version of 3DSLIB that doesn't cause this, I'll be more than happy to remove the nugatory material definition. OK? Cancel?