VMD-L Mailing List

From: Murpholino Peligro (murpholinox_at_gmail.com)
Date: Fri Mar 09 2012 - 11:09:08 CST

@Ana: thanks a lot for all the suggestions!!

@All: now it works...nice and smooth ..

Greetings

2012/3/9 Ana Celia Vila Verde <acavilaverde_at_gmail.com>

> Hi,
>
> Here are a few suggestions to improve your script:
>
> # "file" is a command in tcl; I'm not sure you can name a variable "file",
> like you had...
> set outfile [open "ca-dist.dat" w]
>
> for { set i 2 } { $i <= 111 } { incr i } {
> # Since you only want the average distance between consecutive alpha
> carbons, you don't need the second loop
> # Note that you should always use curly brackets when using expr; your
> code will run much faster
> set j [expr {$i -1}]
>
> # Do the selections this way so you can delete them at the end of the
> loop. This is good practice to save memory.
> set seli [atomselect top "protein and name CA and resid $i"]
> set selj [atomselect top "protein and name CA and resid $j"]
>
> # now getting the index
> set indi [$seli get index]
> set indj [$selj get index]
>
> set dist 0 ;# not sure if this line is correct ; # it
> doesn't hurt
>
> # Just quotes should be sufficient. Alternatively you can write set
> dist [ measure bond [list $indi $indj] ]
> # Note that this returns the distance for the top molecule in VMD
> and for the current frame
> set dist [ measure bond "$indi $indj" ] ;
> puts $outfile "$j $i $dist"
>
> # delete selections to save memory
> $seli delete
> $selj delete
> }; # for i
> close $outfile
>
> I hope this helps. Cheers,
>
> Ana
>
>
> On 3/8/12 10:33 PM, Murpholino Peligro wrote:
>
> Hi all!
> I want to know the average distance for alpha carbons in my protein with N
> residues (in this case 111)
> I was trying to get the distance for residue i and that of residue i-1
> Until now I have>
> set file [open "ca-dist.dat" w]
> for { set i 2 } { $i <= 111 } { incr i } {
> set j 0
> for { set j [ expr $i - 1 ] } { $j <= [ expr $i -1 ] } { incr j } {
> set seli [[atomselect top "protein and name CA and resid $i"] get
> index]
> set selj [[atomselect top "protein and name CA and resid $j"] get
> index]
> puts "$j $selj $i $seli" ;# everything is ok 'til here
> set dist 0 ;# not sure if this line is correct
> set dist [ measure bond {"$selj $seli"} ] ;# I think the problem
> are the double quotes, but I really don't have idea
> puts "$j $i $dist"
>
> }; # for j
> }; # for i
> close $file
> Any help with the code is appreciated
> loading the ca-dist.dat into R in this way I can get the average distance
> very easy and do some plots
>
> Ps ca-dist.tcl is somewhat different of what I want
>
> --
> Mr. Murpholino X
>
> "mi segundo nombre es Peligro!!"
>
> 

-- 
Mr. Murpholino X
"mi segundo nombre es Peligro!!"