VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed May 13 2015 - 16:29:28 CDT

That isn't a complete for loop (should have a closing brace.). Beyond
that, atomselections should happen outside the loop if at all possible.
Atomselections within a loop need to be deleted to free up VMD internal
memory, as they aren't *just* tcl objects, but also create
datastructures within VMD that are not automatically deleted when the
tcl atomselection object goes out of scope. What exactly are you trying
to do? The way I've interpreted the code, you have a bunch of Silicon
atoms, but if they are close enough to an oxygen, you want them to be a
carbon instead (alchemy! VMD doesn't like alchemy), and only for that
frame. Is that correct? Now you've muddled it a bit, since your $all
variable is never called outside of changing its frame, which does
nothing, and $a points to an atomselection that is always at the last
frame, so I can't read your intent. Could you perhaps elaborate on what
problem you are trying to solve?

On 05/13/2015 04:22 PM, JeJoon Yeon wrote:
> There was mistake in previous email. My for-loop looks like
>
> for { set i 0 } { $i <= $nf } { incr i } {
> set a [atomselect top "index < 1338 and name Si and y>9 and within 5
> of atom O]
> set all [atomselect top all]
> $all frame $i
> $a set name C
> $a set type C
> $a set element C
>
> But I still think my way of writing is wrong...
>
> 2015-05-13 14:44 GMT-04:00 Josh Vermaas <vermaas2_at_illinois.edu
> <mailto:vermaas2_at_illinois.edu>>:
>
> Also, you need to make sure your for loop is doing this sanely.
> Here is how I'd approach it:
>
> set a [atomselect top "index < 1338 and name Si and y>9 and within
> 5 of atom O]
> set t [atomselect top all]
>
> for { set i 0 } { $i < [molinfo top get numframes] } { incr i } {
>
> $a frame $i ; #changes the frame the selection will be based on
> $a update ; #Rechecks that its selecting the right stuff
> $a set name C
> $a set type C
> $a set element C
>
> }
>
> However name, type, and element are not per-frame fields, so you
> do know that you'll be changing it for all of them, right?
> -Josh
>
>
> On 05/13/2015 01:07 PM, Maxim Belkin wrote:
>
> Hi,
>
> Have you tried the following?
>
> animate write xyz output.xyz beg 0 end -1 waitfor all
>
> Maxim
>
>
> On May 13, 2015, at 12:53 PM, JeJoon Yeon
> <sonicturbulent_at_gmail.com
> <mailto:sonicturbulent_at_gmail.com>> wrote:
>
> Hello all
>
> I can swap specific atoms for a single frame xyz only. Like
>
> mol new test.xyz type xyz waitfor all
> set a [atomselect top "index < 1338 and name Si and y>9
> and within 5 of atom O]
> $a set name C
> $a set type C
> $a set element C
> set t [atomselect top all]
> $t writexyz swapped.xyz
>
>
> But how can I do this with multiple frame? I tried to use
> for loop but
> 1) Sometimes it causes error
> 2) Sometimes it swaps the specific atoms for all frames,
> but the criteria is based on only last frame's xyz position.
>
> So I don't know what to do anymore. Can anyone help or
> modify that single frame code to work for multiple frames?
> Is this coming from read / write problem?
>
> Thanks
>
> Best,
>
>
>
>