VMD-L Mailing List

From: ban arn (ban.arn_at_gmail.com)
Date: Mon Mar 21 2011 - 10:37:03 CDT

Dear VMD users

Thanks for reply.

But would like to do the same (projection of c-aplha atom coordinates
on xy plane) for trajectories.

I tried this script

set mol [molinfo top]
set out [open xy_cordinates.txt w]
 set sel [atomselect top "protein and name CA"]
 $sel get {x y}
 set frames [molinfo $mol get numframes]
 for {set i 0} {$i < $frames} {incr i} {
  $sel frame $i
  $sel update
  puts $out "$i $x $y"
}

I didn't get any result in the output file.

Any help is greatly appreciated.

Many Thanks
Balaji

2011/3/18 Paweł Kędzierski <pawel.kedzierski_at_pwr.wroc.pl>:
>
> On 18.03.2011 18:58, ban arn wrote:
>>
>> Dear VMD users
>>
>> I would like to know is there any script available in vmd or from
>> others sources for projection of c-aplha atom coordinates on xy plane.
>>
>
> Did you mean filtering out CA atoms and replacing z coordinate with 0 (or
> whatever)? E.g.:
>
> awk --posix '/^ATOM  (.){6} CA /{printf("%.46s%8.3f\n",$0,0);}'
> your_file.pdb
>
> Or if you filtered out CA previously (within VMD, File->Save coordinates,
> selection "protein and name CA") it would be enough to say:
>
> awk '{printf("%.46s%8.3f\n", $0, 0);}' your_file.pdb
>
> This works with gnu awk.
> HTH
> Pawel
>>
>> Any help is greatly appreciated.
>>
>> Many Thanks
>> Balaji
>>
>