A description this bugs I find in the python bug tracker as 'waitvariable hangs at exit'. The automation works based on the fact that you can load a molecule in vmd using the tk console. Im using Spyder IDE, and bugs see in spyder console, wherein run repeatedly my code. You can load them manually, or automate it using a tcl script. Remember, Tcl's generic syntactic parsing happens first, before command arguments are interpreted semantically. A message in console: invalid command name '66120320callit' while executing '66120320callit' ('after' script) Sorry for my small information in first post. Without quoting, Tcl doesn't know that that's meant to be one word the generic parsing layer decides there's really four words there ( set, ag_around_water, resid and the complex ) and tells set to deal with that, which it doesn't like. It's usually best to avoid using them like that. Now, spaces are legal in variable names, but then the variable name needs to be quoted, and that can get a bit annoying. Has what appears to be a space instead of an underscore in the variable name. vmd 2igd.pdb Tk console source vector1. However, in this case we can look through and see that this line near the bottom of the script: set ag_around_water resid commands.vmd README.md VMD scripting Tips Show the list of available render commands render list Delete graphics graphics top delete all Drawing arrows arrow1/ A simple TCL script to draw arrows. If you examine the stack trace (usually printed with the error message when using standard tclsh, though it's changeable with user code) then you'll get told where the problem happened. The consoleinterpcommand in the console interpreter allowsscripts to be evaluated in the main interpreter. arms: Position a set of XYZ axes on of screen. Home selected as (options) may not be available is the electricity version of VMD.animate: Play/Pause/Rewind a molecular trajectory. In this case, it's coming from the set command, and indicates that you've either said set on its own, or given more than two further arguments to it. VMD Text Menu Summary VMD understands commands which start with the following words click on an command for a more complete synopsis. if you want a more automated way, then you need to know the exact atom name and the residue number. where x is the index of the atom of an residue in which you are interested.
Is a standard error thrown when a built-in command gets the wrong number of arguments to evaluate. 1 Answer Sorted by: 3 topo addbond x y should do the trick. Wrong # args: should be "set varName ?newValue?" Puts $outfile "$pid $k] $ag_around_water_resname A: $water_around_b_resname" #count water molecules between chain A and chain C or between #chain B and chain C Note: The script includes terms specific to VMD program, such as mol and resid. I tried to run the following Tcl script and got the error: wrong # args: should be "set varName ?newValue?"
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