Rendering CG helices & sheets with VMD
- Details
- Last Updated: Thursday, 12 June 2014 15:31
We gathered and extended the set of small Tcl scripts available in our group to draw protein secondary structure in VMD-like fashion.
The script can be found here: cg_secondary_structure.tcl
Usage
After sourcing the script in VMD (source /path/to/cg_secondary_structure.tcl), two routines are available from the command line: cg_helix and cg_sheet. The options and default values are listed below. You can summon an "how to" at any moment by calling the cg_secondary_structure_usage command.
This script needs the La package, a linear algebra package written by Hume Integration Software, used here to compute principal axes of helices/sheets; the package is freely available at http://www.hume.com/la/. After downloading it, extract and source the la.tcl file in VMD.
You can give an output of do_dssp as an input for this script; it will be parsed and this script will try to draw each helix/sheet. If you use this option (-ssdump), you can leave the first list empty (see examples).
cg_helix
Usage:
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vmd > cg_helix {{start1 end1} {start2 end2} ...} [OPTIONS]
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Where start and end are respectively the first and last residues composing an helix; you can provide more than one helix, as shown in the command line. The "{" and "}" characters are mandatory for Tcl to understand it as a list!
Options and default values:
| -molid | "top" | VMD-defined ID of the molecule to process |
| -ssdump | "ssdump.dat" | read topology from a do_dssp-formated file |
| -bbbname | "B.*" | backbone bead name |
| -hlxmethod | "idealhelix" | method to draw sheets "idealhelix", "realhelix" or "cylinder" |
| -hlxcolor | "red" | color of helices |
| -hlxmat | "Opaque" | material |
| -hlxres | 12 | resolution |
| -hlxrad | 2.0 | radius of cylinders |
| -hlxsides | "round" | arrow sides "round" or "sharp" |
| -hlxfilled | "yes" | cylinders filled or not "yes" or "no" |
| -hlxstep | 1.0 | angle step size |
| -hlxthick | 0.2 | thickness of helix |
| -hlxwidth | 2.0 | width of helix |
| -hlxdirect | "no" | draw the director vector of the helix (or not) |
| -hlxdirrad | 0.1 | radius of the cylinder (director) |
| -hlxdirclen | 0.3 | length of the cone (showing direction of the director) |
| -hlxdircrad | 0.2 | cone radius |
| -hlxsecbprop | 0.5 | proportion of the preceding/following bond used as length for starting/ending flat cones |
Example:
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vmd > cg_helix {{5 48} {120 146}} -hlxmethod "cylinder" -hlxcolor "lime" -hlxrad 2.5
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cg_sheet
Usage:
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vmd > cg_sheet {{start1 end1} {start2 end2} ...} [OPTIONS]
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Where start and end are respectively the first and last residues composing a sheet; you can provide more than one sheet, as shown in the command line. The "{" and "}" characters are mandatory for Tcl to understand it as a list!
Options and default values:
| -molid | "top" | VMD-defined ID of the molecule to process |
| -ssdump | "ssdump.dat" | read topology from a do_dssp-formated file |
| -bbbname | "B.*" | backbone bead name |
| -shtmethod | "flatarrow" | method to draw sheets "cylindarrow", "flatarrow", "bendedarrow" or "triangle" |
| -shtcolor | "green" | color of sheets |
| -shtmat | "Opaque" | material |
| -shtres | 12 | resolution |
| -shtsides | "round" | sheet sides "round" or "sharp" |
| -shtrad | 0.4 | radius of cylinders |
| -shtconrad | 0.8 | radius of arrow cones |
| -shtlencone | 1.5 | length of arrow cones |
| -shtfilled | "yes" | cylinder filled or not "yes" or no" |
| -shtarrwidth | 2.0 | width of arrows |
| -shtheadsize | 4.0 | size of the arrow heads |
| -shtarrthick | 1.0 | thickness of arrows |
| -shtstep | 0.1 | distance step size |
| -shtthick | 0.2 | thickness of sheet |
| -shtwidth | 2.0 | width of sheet |
| -shtdirect | "no" | draw the director vector of the sheet (or not) |
| -shtdirrad | 0.1 | radius of the cylinder (director) |
| -shtdirclen | 0.3 | length of the cone (showing direction of the director) |
| -shtdircrad | 0.2 | cone radius |
| -shtsecbprop | 0.5 | proportion of the preceding/following bond used as length for starting/ending flat cones |
Example:
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vmd > cg_sheet {} -shtfilled "no" -ssdump protein.dat -shtarrowthick 0.4
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Known issues
There is still a bunch of small graphical issues (thanks to drop a mail to the contact at the bottom of this page whenever you find something... unexpected); sheets are particularly ugly. It's not the priority right now, it will be fixed when we will have time... keep checking this page and your version of the script updated! We are writing this tool for personal purpose, and we didn't retroactively test all the graphical options and the result when mixing them together. Thanks to do that for us!
- Drawings do not follow the protein dyamic along a trajectory; you need to redraw everything at each step (no ways to change this behavior so far).
- The "bendedarrow" (sheet style), which would be the closest to VMD atomistic drawings, doesn't work so well so far. Still working on it!
- If an helix is too bended, VMD will not be able to draw it using the "idealhelix" or "realhelix" method (the script will output an error message with the termini of the helix).
- Not able to draw helices smaller than 3 residues (!).Fixed. Avoided.
- Tcl needs an empty line at the end of the files it reads!
- On the same level, Tcl seems to understand differently simple and double quotes... Please check that before shouting.
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