the pdb ( ) ( 1 ) currently contains > 30 000 3d structures of bio - molecules ( march 22 , 2005 ) .
those who want to look at one of these 3d datasets need additional software to visualize the structure file that is stored in the database .
modern web browsers like mozilla , internet explorer or opera normally display only html code and images directly . in order to display other complex data
these software components could be java applets , plug - ins or an external helper application .
the disadvantage of java applets and plug - ins embedded into the layout of the displayed webpage by the web browser is the low resolution of the images  normally < 100 d.p.i .
( dots per inch ) . often screenshots made for publications are not accepted for printing .
thus people need to install dedicated programs for rendering molecular pictures , but often these programs are difficult to use and a lot of the functions can only be activated by programming scripts .
this is only acceptable for intensive use and not for use from time to time . a pioneering webpage from 1995 called 
molecules to go ( ) combines a full text within the pdb with a simple structure presentation and the jena image library database ( ) ( 24 ) offers for the generation of mono or stereo pdf images with a fixed representation style either in a default orientation or via a vrml interface in a user - selected orientation , a related option that is based on molscript . at the moment
there is no way to get a high quality and high resolution 3d structure image with a user - selected view of a molecule via internet without using additional locally installed software .
the alternative concept splits the web interface ( client ) from the rendering program ( server ) .
the web browser only gets html and javascript code ( which normally every browser can handle ) and an image of the molecule ( figures 1 and 2 ) .
the user has different methods to upload a 3d structure of a molecule in pdb format to the web applications server .
the pdb format contains , next to the atom type , the x , y and z co - ordinates of the 3d structure . for manual file
in addition to this method a pdb file can be fetched by the four - character pdb i d . unless the files are stored locally they are automatically downloaded from the protein database server .
furthermore , aismig ( an interactive server - side molecule image generator ) provides a simple object access protocol ( soap ) interface to be fully integrated with other web applications available on the internet .
thus molecules generated on other servers or stored in other databases can be automatically uploaded to the aismig server and directly accessed for the rendering process .
see the carbohydrate builder web tool sweet ii ( 5 ) ( ) as an example . at the server side ,
a script fetches the request from the user and after checking if the file is in pdb format , a script calls the free program pymol ( ) to generate the molecular image . at this first stage the user can manipulate the color and shape of the molecule interactively .
the menu structure ( figure 3 ) is quite similar to the rasmol ( 6,7 ) menu panel and provides the standard manipulation functions
. the user can access parts of the protein by atom number , atom type , group name , group number and chain .
coloring by structure ( coloring the sheets , turns and loops ) is also possible .
for the shape of the molecule we provide the following modes : line , sticks , ribbon and cartoon ( only proteins ) , sphere , surface , dots and mesh .
static macros like color by b - factor or color by eisenberg hydrophobic scale are the same for all molecules .
dynamic macros , in contrary , are generated dynamically at starting time by other service programs .
therefore the program needs to analyze the molecule and writes the appropriate data to the dynamic macro .
if the user has the molecule in the right perspective , he switches to the second stage where he needs to set the rendering options . at this point pymol produces the molecule as a set of 3d objects that are loaded and parsed by the second stage program part . at this stage
, the user can only influence the rendering and scene parameters like image size , additional spotlight or texture elements .
the raytracer for generating the high quality and high resolution pictures is the free program povray ( ) .
if all settings are established , the user can start the process of rendering the final image . for this process
he needs to enter his email address and he gets an email with a link to the result page . until the image is ready , the user can see the progress ( as a percentage ) if the job is running , or the queue position that is displayed .
the web server submits the rendering job to a small linux cluster where a modified version of povray runs .
an alternative method of internet - based display of 3d structures of molecules has been developed .
the aismig web application is an implementation of this alternative concept and the free service is available at .
figures 3 and 4 illustrate the object generation at stage 1 , the object rendering at stage 2 and the final image .
figure 5 demonstrates the different possibilities of the web application . by uncoupling the object generation from the object rendering it is possible to manipulate the scene and add a second light source or map some textures on the molecule .
( some nice images can be found at the aismig homepage in the art gallery . )
the aismig services can easily be linked to other web applications or databases by using the soap interface in order to upload a 3d pdb file to the webserver .
an example of how to connect to another web - application by this mechanism is demonstrated by the sweet ii ( 5 ) carbohydrate builder web tool where the user can create 3d structure files of carbohydrates and can visualize the generated structure by aismig .
the concept has advantages and disadvantages , as does every concept . in the following section
the alternative concept will be discussed by comparison to other current concepts like java applets , plug - ins and external helper tools .
java applets have the advantages that they are nearly independent of browser and operating system .
the standard java applets for molecule visualization are jmol ( ) , webmol ( 8) ( ) and pdbjviewer ( 9 ) ( , ) .
pdbjviewer is the latest applet and uses the java3d extension for surface generation . at the moment
the java virtual machine is a plug - in for web browsers but in former times this was different hence it is listed in the table at this point .
the most often used plug - in for visualization of molecule 3d structures is chime ( ) but plug - ins are highly operating system and browser dependent .
also , java applets as plug - ins are not able to generate high - resolution images besides they need to be installed on the client system .
one advantage of these methods is that the applet or the plug - in are included in the layout of the web page and can interact with other components .
the advantage of external programs is that they can render large images and often they have powerful functions for working with small molecules or with proteins .
there are lots of programs for displaying 3d structures of molecules and normally every molecular viewing program can be used by this mechanism ( that the webserver calls an external helper program with a file name as parameter ) .
the most popular programs are : rasmol ( and ) , swiss - pdb viewer ( 10 ) and pymol .
the greatest advantage of the interactive server - side image generation concept ( aismig ) is that no additional software in addition to the web browser is necessary to view and process the molecules , thus everyone can visualize and manipulate the generated molecule structure . furthermore rendering a molecule in high resolution ( e.g. 1200 d.p.i . ) for a publication or poster poses no problem .
software modules need only be installed once at the server side and all users of the service can use it . by using pymol for image generation
it is possible to generate complex surfaces as pymol uses opengl with all its advantages .
however , this server - side image generation method requires for each interaction a request to the server and at every interaction an image is generated and transmitted to the client .
the images are small but the sum of all can be quite large . at the moment
aismig sends a jpg image with an average size of 15 kb for each request . with one of the menu entries the user can download a png image in a better quality that is 60 to 140 kb .
it is slower than client - side running software where real time rotation by mouse movements is possible .
an alternative concept similar to the current concepts ( java , plug - ins and external application ) was developed and implemented .
aismig will complement the current concepts with its advantages ( no additional software installation and rendering of high - resolution pictures ) , but it was not designed to replace any of the existing methods for molecule visualization .
aismig enables the possibility to visualize a molecular 3d structure with only a standard web browser without requiring local installation of any additional structure viewer software .
aismig helps even those who are not computer experts to see 3d molecule structures provided by a web service or web - based databases .
1a0s  sucrose - specific porin rendered in high quality and high resolution 4650  3300 pixel with the  color by rainbow function .
 using a web browser without additional software and generating interactive high quality and high resolution images of bio - molecules is no longer a problem . interactive visualization of 3d molecule structures by internet browsers normally is not possible without additional software and the disadvantage of browser - based structure images ( e.g. by a java applet ) is their low resolution . 
 scientists who want to generate 3d molecular images with high quality and high resolution ( e.g. for publications or to render a molecule for a poster ) therefore require separately installed software that is often not easy to use . 
 the alternative concept is an interactive server - side rendering application that can be interfaced with any web browser . 
 thus it combines the advantage of the web application with the high - end rendering of a raytracer . 
 this article addresses users who want to generate high quality images from molecular structures and do not have software installed locally for structure visualization . often people do not have a structure viewer , such as rasmol or chime ( or even java ) installed locally but want to visualize a molecule structure interactively . 
 aismig ( an interactive server - side molecule image generator ) is a web service that provides a visualization of molecule structures in such cases . 
 aismig - url : . 
INTRODUCTION
MATERIALS AND METHODS
RESULTS
DISCUSSION
CONCLUSION
Figures and Tables