At my request, Tim Maffett was kind enough to fix four of these five limitations in scripts saved from Chime version 2.0. (He didn't fix the dot surfaces because I hadn't discovered this bug in RasMol at the time. Dot commands can be added to the scripts after they are saved to generate any desired dot surfaces.)
Scripts saved from Chime contain a few commands which don't exist in RasMol. Nevertheless, Chime-saved scripts run satisfactorily in RasMol. RasMol emits error messages about the commands it does not recognize, but proceeds through the entire script.
Scripts saved from RasMol or Chime tend to be unnecessarily long. Such scripts may take on the order of a full minute to execute in the Protein Explorer in default mode, where messages are discarded. If you request that all the script commands be echoed to the message box, unscrambling of the message stream can take more than 15 minutes! Even in RasMol, with large molecules and complex images, the RasMol-saved script can sometimes take minutes to generate the image.
The reason that these scripts are so long is that they often contain hundreds of select commands, each followed by rendering and coloring commands. In the worst cases, selection proceeds atom by atom.
Most sections of these scripts execute quickly. As mentioned above, it is the section containing the selection, rendering, and coloring commands which is unnecessarily long -- a section subtitled # Atoms. Therefore one can shorten such scripts greatly by editing them to replace the unnecessarily numerous commands with simpler commands which do the same job. A concrete example will best illustrate how to do this.
I generated an image in the Protein Explorer, and then I saved a script. In RasMol, the same example could be used with a few minor modifications. The PDB file employed, 105D, contains eight models of an unusual DNA structure obtained from NMR analysis. After I experimented with different commands to get an image I liked, I summarized the commands needed to select, render, and color the desired atoms as follows:
#SUMMARY OF SELECTION, RENDERING, COLORING wireframe 0.2 select t color yellow select c color red select backbone color white select phosphorus color cpk spacefill 0.8 restrict model=1 and not hydrogenBefore saving the script, I had used the mouse to set an orientation and zoom which I liked. The saved script contained 1,142 lines and began as follows:
#!rasmol -script # File: \s3vv9qel. # Creator: Chime Version 2.0 set load check on load pdb "105d.pdb" background [255,255,255] set ambient 60 set specular off reset slab off rotate z 171 rotate y -80 rotate x -172 translate x 1 zoom 167 center all translate center center set zoom center true set bonds off set axes off set boundingbox off set unitcell off set bondmode and dots offI deleted everything after the above commands and added the above "summary" commands, making a script file with only 39 lines. On my computer the Chime-saved, 1,142-line script took 20 seconds to generate an image, plus another 20 seconds before the PE became "ready" (with Message Control: Scripts called from the command slot unchecked!), a total of over 40 seconds. In contrast, the manually modified script took less than 3 seconds to produce the same image and become "ready".
In some cases, in order to achieve the desired result, you may need to replace just the # Atoms section with your summary commands, preserving the sections at the end entitled
# Ribbons # Backbone # Labels # Monitors # Definitions # Current Selection