![]() Remember, Tcl's generic syntactic parsing happens first, before command arguments are interpreted semantically. 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. However, in this case we can look through and see that this line near the bottom of the script: set ag_around_water resid 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. 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. Is a standard error thrown when a built-in command gets the wrong number of arguments to evaluate. Wrong # args: should be "set varName ?newValue?" These settings are applied by the systemd-vconsole-setup service, which is essentially a glorified way of running setfont and loadkeys before the login services are brought up. set fp open 'input. The way to do this on a systemd operating system is to edit the font settings in the /etc/nf file. If you want to rotate the residue and save the new coordinates, you have to rotate it using the 'Move'. ![]() When other text (e.g., from a mouse pick) is displayed. This window normally contains the prompt vmd >. Text commands can be entered into VMD in several ways: Commands can be entered by typing them at the VMD prompt in the text console window. But when I tried to open that file manually in that working directory folder, it is not even shown in it. On VMD TK console use the following commands set all atomselect top 'protein' set all atomselect top 'protein and res id 1-20' Cite Top contributors to discussions in this field Nidhal. I think, using TK console you will get only visualization of the rotated structure. Next: Tcl/Tk Up: Tcl Text Interface Previous: Tcl Text Interface Contents Index Using text commands. when I type command 'dir' on tk/tcl console, it shows file name which I am trying to generate. Puts $outfile "$pid $k] $ag_around_water_resname A: $water_around_b_resname" I am trying to write a file using tcl scripting (Via VMD). 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. #count water molecules between chain A and chain C or between #chain B and chain C 1 Answer Sorted by: 3 topo addbond x y should do the trick. 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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