Output

From MarcsHomepage

The file output of a molecular modelling software-package is usually meant for use in publications rather than for interactive viewing. Therefore it isn´t important if one program needs much more time to generate the final image than another program. Quality is the thing we are looking for.

External Rendering

Things have changed since my first review of output-capabilities of the programs mentioned in my list. Almost every viewer can now produce output for a rendering package (mainly POVRay) and therefore the differences in image quality have become almost a matter of taste.

One could think that they must be identical when using the same technique (i.e. raytracing with POVRay), but there is still a difference between the output of f.e. Molmol, Rasmol, SwissPDBViewer and Molscript, related to the different approach of generating POVRay-input.

Especially the quality of irregular surfaces and triangulated meshes, used for drawing of ribbons and molecular envelopes is a bit different, and the programs differ also in the quality of the POVRay-output (frequency of smaller glitches and errors in the coordinates or the naming of objects, camera and lighting defaults to name a few).

Still Molmol holds the crown for simple, out-of-the-box rendering with a nearly WYSIWYG-interface (the POV-image looks exactly the same as the OpenGL-view, regarding color, size, field of view and lighting (mostly) of the scene). WebLabViewer is good as well, and SwissPDBViewer still has some minor problems which need some handwork (lighting, camera-placement, some minor problems with naming of HETATMS).

Pymol has it's own internal renderer which is good enough for almost every task and also produces very good images "out of the box". A big drawback (and a big plus to SwissPDBViewer imho) is the fact, that Molmol-generated POV-files are a bit unstructured, whereas SwissPDBViewer generates neat, easy-to-edit POV-files, complete with annotations, split into two sections (coordinate data and environment settings (color, lighting, texturing, surrounding and so on, which are normally the parts you might want to edit afterwards)).

Screenshots

All other programs I have listed in my short review can also export images, but only of the same quality as the interactive display. There are several pixel-file-formats supported in every package (gif, bmp, jpg) and WebLab Viewer Lite can also export to VRML -which isn´t good for high quality image-generation, but for Internet-presentation.

On the lower end of the scale are Rasmol and Chemscape Chime, which is based on Rasmol´s graphics engine. Rasmol nowadays has an experimental POVRay-output, which does not work very well and cannot export secondary structure elements like ribbons, but it is a step in the right direction. Hopefully this will improve in the future.

Molscript can use another renderer, specially designed for the display of molecular structures, Raster3D, which produces nice images. Raster3D is the de-facto standard for crystallographic publications of ribbon and ball-and-stick images of macromolecules.

JWYOE

Judge With Your Own Eyes: I have provided some close-ups of the maximum-quality output of all programs listed, so that you can compare their output-quality by yourself.

Note: The images are not up-to-date, WebLabViewer and Pymol are missing, and the Raster3D-output of Molscript is not shown (instead a rasterized Postscript-image has been used).

The POVRay images might be far from optimum, because I am not a POVRay-expert, so that the real coloring and shading of these pictures may be not at optimum quality.

Molmol out.jpg Spdbv out.jpg
Wlview out.jpg Rasmol out.jpg
Molscript out.jpg Gopenmol out.jpg
Icmlite out.jpg

Fig. 1: Shown are the differences of the output of the programs mentioned above (from top-left to bottom-right: Molmol (POVRay), SwissPDBViewer (POVRay), WebLabViewer (Screenshot), Rasmol (Screenshot), Molscript (old version, converted from eps-output)), gOpenmol (screenshot) and ICMLite (screenshot). You can see some quality-differences between the POVRay-rendered pictures, concerning smoothness of the surfaces (especially the alpha-helices) due to the fact, that the programs use different algorithms to triangulate the surface of the ribbon-objects. The output of gOpemol and MCILite is quite nice because they utilize the OpenGL-library for real-time-display (afaik you can´t change the predefined color for secondary structures in WebLabViewer). Rasmol has it´s own (very fast) realtime-renderer, but the output isn´t of high quality. The output from Chemscape Chime is similar to that of Rasmol (but one would not use this plugin for image-generation, is´s mainly intended for online-viewing). All pictures are displayed at full size -no post-processing (smoothing, resizing, color-correction) has been done (except for the Molscript-image, which has been converted to *.jpg-format with Photoshop). Dataset used for image-generation was 1vac.pdb from the Brookhaven Protein Database