ConSCRIPT

Abstract

The aim of the Structural Biology Extensible Visualization Scripting Language (SBEVSL) project is to allow users who are experts in one scripting language to use that language in a second molecular visualization environment without requiring the user to learn a new scripting language. ConSCRIPT, the first SBEVSL release, is a plug-in for PyMOL that accepts RasMol scripting commands either as premade scripts or as line-by-line entries from PyMOL's own command line. The plug-in is available for download at http://sourceforge.net/projects/sbevsl/files in the ConSCRIPT folder.

There are many excellent visualization programs used in structural biology [1]. Most come with their own scripting languages that permit both command-line control and the packaging of complex sets of display commands in a file. Coordination among multiple visualization programs is often necessary in the course of a single investigation and in combining results from multiple investigations. If two programs use different scripting languages, valuable time can be lost learning the new scripting language. The long-range goal of the Structural Biology Extensible Visualization Scripting Language (SBEVSL) [2] project is to make common molecular visualization tools available to the broadest possible audience, so that each user can use many programs, with knowledge of the scripting language for only one of those programs. Three of the most popular molecular visualization programs are Jmol [3], PyMOL [4], and RasMol [5, 6]. All are open source programs, making them ideal initial targets for establishing a common scripting language. Jmol, the most popular of the three, already uses a variant of the RasMol scripting language. Chime [7], a proprietary version of RasMol, also uses a variant of the RasMol scripting language. For many educators and scientists, PyMOL is the application of choice for preparing images and animations of their structures because of the beauty and quality of the images. Therefore, making the RasMol scripting language work with PyMOL will have a significant unifying impact. RasMol's scripting language is known for ease of use and a natural language interface. However, its interface was implemented in 1993 and does not take full advantage of today's graphics processing units. Nevertheless, it is still widely used on computers running Windows, Linux, or Macintosh operating systems. PyMOL is a much newer and more versatile 3D molecular visualization environment. Its graphics are much more advanced and have become the standard in today's captured images. However, its scripting language is based on object-oriented Python and can be difficult for someone unfamiliar with computer science to learn. It is also a complex language with many more commands than RasMol's simple language.

Design Principles

To create a RasMol command interpreter for PyMOL (the first goal of the SBEVSL project), we compared the command sets for RasMol and PyMOL, then created ConSCRIPT, a plug-in for PyMOL that accepts RasMol script files and commands, translates the commands, and executes them in PyMOL. The process involves searching for recognized, valid, RasMol script commands and performing their PyMOL equivalents, either as single commands or as a series of commands that produce the same result. Several commands that are most commonly used in RasMol are listed in Table I, shown along with their PyMOL equivalents.

Table I. A list of commonly used commands available in RasMol and their equivalents in PyMOL represented as either a single command or as a series of commands.

RasMol	PyMOL
Backbone	Set Ribbon_sampling, 20
	Set Ribbon_smooth, 1
	Set Ribbon_width, 0.02
	Show ribbon, <selection>
Background	Bg_color <color>
Cartoon	Cartoon rectangle
	Show cartoon, <selection>
Center	Center <selection>
Map generate	Map_new <name>, <type>, <grid>, <selection>
	Isomesh/isodot <name>, <map>, <level>, <selection>
	Zoom
Map zap	Delete <map>
Rotate	Rotate <axis> <angle>
Script	Run [script]
Select	Select <selection>
Spacefill	Show spheres, <selection>
Wireframe	Show sticks, <selection>

As we considered which commands to translate, it became clear that a number of features in PyMOL should be added to RasMol to make the two programs more complementary. To overcome this difference and to facilitate movement between the programs, several new features have been implemented and are now supported in RasMol [8]:

• SBEVSL movie commands [9].

• Electron density maps [10].

• Lee–Richards surface approximation by contouring pseudo-Gaussian electron densities [11].

We used a variety of coding methods to correlate RasMol commands to their PyMOL command equivalents. When a single command could be directly translated, we used simple code to recognize that command and perform its equivalent. For RasMol commands containing multiple parameters, the command was translated into a series of PyMOL commands, which were executed sequentially. Several commands required altering PyMOL's default settings to produce exactly the same results. Moreover, several commands remain untranslated for various reasons including lack of universal features to mimic a RasMol code in PyMOL, and intentionally untranslated commands that would only serve to confuse users, such as help, where returning the PyMOL help would be of no use to a ConSCRIPT user. The untranslated commands are Bulgarian, Chinese, English, French, Italian, Japanese, Russian, Spanish, Clipboard, Colourmode, Connect, Help, Load Inline, Molecule, Notoggle, Pause/Wait, Print, Renumber, Show, Star, Strands, and Structure.

Features

Script Loading Interface

Once ConSCRIPT is installed, it automatically loads whenever PyMOL opens. The user can load a RasMol script file by selecting ConSCRIPT from the Plug-in drop-down menu. This opens a dialog box that will enable the user to search for the script file. The converter sequentially executes the given RasMol commands on any protein already loaded in PyMOL. As an alternative, users can reinitialize PyMOL and include commands for loading the protein in the RasMol script.

Command Line Interface

With ConSCRIPT installed, users can enter RasMol commands directly on PyMOL's own command line. To execute RasMol commands from PyMOL's command line, begin the desired command with the token “VSL” followed by a space and then the desired command; users can also enter a Rasmol command prefaced by “r,” “R,” “rasmol,” or “RASMOL,” That command will then be converted using the same algorithm as the script converter and executed immediately. Requiring one of these tokens allows the user to switch between RasMol and PyMOL commands at will and prevents ambiguities between similar RasMol and PyMOL commands.

Implementation

The image of porcine pancreatic elastase in Fig. 1 was generated using a RasMol script in RasMol. The protein is shown in a cartoon representation with the catalytic triad and a bound inhibitor highlighted as wireframes. Table II contains the RasMol and PyMOL scripts used to produce Figs. 1, 2, and 3. The script used to produce Fig. 1 was then converted to a PyMOL script so as to create the same output from PyMOL, which is shown in Fig. 2. Then, the same RasMol script was used to reproduce the image from Fig. 1 using the ConSCRIPT plug-in for PyMOL, as seen in Fig. 3.

Fig. 1.

View of the active site of a serine protease with a bound inhibitor (porcine pancreatic elastase [12], PDB entry 8est) that was generated by RasMol using a RasMol script.

Table II. Translation of a set of RasMol commands into the scripting language of PyMOL using ConSCRIPT.

Rasmol command	PyMOL equivalent
load “/path/to/file/8est.pdb”	load “/path/to/file/8est.pdb” rotate ×, 180
background white	bg_color white
select all	select all
wireframe off	hide sticks, sele; hide lines, sele
restrict not water	hide everything, resn hoh
select helix	select ss h
cartoon 200	show cartoon, sele
color magenta	color magenta, sele
select sheet	select ss s
cartoon 200	set cartoon_rect_length, 0.8; cartoon rectangle; show cartoon, sele
color yellow	color yellow, sele
select protein and not helix and not sheet	select not (ss h or ss s)
trace	cartoon tube, sele; show cartoon, sele
select gis	select resn gis
wireframe 30	set stick_radius, .24, sele; show sticks, sele
color cpk	no native pymol command for this
zoom 300	zoom all −15
select 57,102,195	select resi 57+102+195
wireframe 30	set stick_radius, .24, sele; show sticks, sele
color cpknew	no native pymol command for this
translate y 10	translate [0,−10,0]

The commands in the first column were used to generate Figs. 1 and 3 and the commands in the second column were used to generate Fig. 2.

Fig. 2.

View of the active site of a serine protease with a bound inhibitor (porcine pancreatic elastase [12], PDB entry 8est) that was generated by PyMOL using a PyMOL script.

Fig. 3.

View of the active site of a serine protease with a bound inhibitor (porcine pancreatic elastase [12], PDB entry 8est) that was generated by PyMOL using a RasMol script translated by ConSCRIPT.

The conversion of RasMol scripts into PyMOL scripts presented many challenges. For example, the two programs load molecules in different orientations. ConScript counteracts this by rotating the molecule 180° about the x-axis immediately after it executes the load command. Also, the operation of the zoom command was different in scale and implementation (linear in RasMol vs. non-linear in PyMOL). Sticky selections are a feature present in RasMol, but not in PyMOL. Our solution to this is quite simple. PyMOL does not recall the last selection automatically, even though it may remember it. ConSCRIPT simply ensures that any command executed is executed on the previous selection by having a variable dedicated to the previous selection and forcing the PyMOL command to act on that selection. The largest difference is in the script format—RasMol uses natural language scripting, whereas PyMOL uses object-oriented code. Finally, there were some RasMol commands (including bond, connect, star, and strands) that did not have equivalents in PyMOL and could not be implemented at the level of a plug-in. The advantage of using a plug-in is that ConSCRIPT is able to work with a wide range of existing PyMOL installations. The plug-in will remain available, but the missing commands will be implemented within PyMOL proper in a future release of open source PyMOL by the SBEVSL project.

The plug-in is available for download as a compressed file in both .tar.gz or .zip formats at http://sourceforge.-net/projects/sbevsl/files in the ConSCRIPT folder. The compressed file contains the plug-in (ConSCRIPT.py), the licensing information, and a readme file in text, html, and pdf formats with instructions for installation in Mac OSX, Windows, and Linux environments. Information on creating publication quality figures using PyMOL commands is included in the readme.txt, readme.html, and readme.pdf files in the compressed file. It is important to note that clicking on the prominent green download arrow on this page (or the main SBEVSL page on SourceForge.net) may lead you to another file that is part of the SBEVSL project. You will need to open the ConSCRIPT folder on http://sourceforge.net/projects/sbevsl/files by clicking on the green triangle to the left of the ConSCRIPT folder. Similarly, you should open the latest ConSCRIPT folder (currently ConSCRIPT-2.1) and download the most recent .tar.gz or .zip file.