VMD-L Mailing List

From: Bryan Roessler (roessler_at_uab.edu)
Date: Thu Apr 19 2012 - 15:17:35 CDT

Thank you! It's always the simple things...

On Thu, Apr 19, 2012 at 2:23 PM, Joaquim Rui de Castro Rodrigues <
joaquim.rodrigues_at_ipleiria.pt> wrote:

> Hi,
>
> The 2nd line of your script is wrong at incr $f
> It should be:
> for {set f $firstFrame} {$f < $lastFrame} {incr f} {
>
> Hope this helps,
> Rui Rodrigues
>
>
> ________________________________________
> De: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] Em Nome De Bryan
> Roessler [roessler_at_uab.edu]
> Enviado: quinta-feira, 19 de Abril de 2012 19:17
> Para: vmd-l_at_ks.uiuc.edu
> Assunto: vmd-l: Problem with hydration script
>
> proc residue_hydration {firstFrame lastFrame} {
> for {set f $firstFrame} {$f < $lastFrame} {incr $f} {
> set sel1 [atomselect top "protein and within 3 of water"]
> $sel1 frame $f
> lappend restotal [lsort -unique -integer [$sel1 get resid]]
> }
> set outDataFile [open hydration.csv a]
> for {set r 1} {$r < 1480} {incr r} {
> set num [llength [lsearch -exact -all $restotal $r]]
> puts $outDataFile "$r,$num"
> unset indnumber num
> }
> close $outDataFile
> }
>
> I'm having a trouble with this hydration analysis script. I'm trying to
> record the number of frames that a particular residue is within 3A of water.
>
> Whenever I run the first for loop, it continues to infinity (crashing VMD)
> although I cannot understand why. I've tried using "animate goto $f" and
> "display update ui" to no avail. Note the use of the "-unique" switch so
> that the residue is only counted once (even if multiple atoms are within 3A
> of water).
>
> It's driving me nuts!
>