VMD-L Mailing List

From: Jianhui Tian (jianhuitian_at_gmail.com)
Date: Sat Mar 31 2007 - 19:50:43 CDT

Hi John,

The "if" appear to be the same line of the "set psi" was just a written
error for this email.

When I run the script with "vmd -dispdev text -e calhbond.tcl", it stopped
with "vmd>", seems to waiting for following commands. I cant figure out what
bug there is. Thanks.

Jianhui

On 3/31/07, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> What error message do you get?
> I suspect you might have a problem with the 'if' statement
> that begins on the same line as the 'set psi' without any semicolon.
>
> Also, if you're running this for batch analysis, you're going to
> need to replace the deprecated "mol load" command with the new
> "mol new" and "mol addfile" commands, in order to guarantee that
> the loading completes before your script commences trying to process
> the data:
>
> # DON'T use 'mol load' anymore, it will be removed from a future VMD
> release
> mol load parm7 $parm dcd $dcdFile
>
> # Use these commands instead, they have long since replaced 'mol load'
> # and are the only way to access various new features that did not exist
> # in the old versions of VMD
> mol new $parm type parm7 waitfor all
> mol addfile $dcd type dcd waitfor all
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Mar 30, 2007 at 03:49:45PM -0400, Jianhui Tian wrote:
> > Hi all,
> >
> > I write a tcl script to calculate the helix content of the peptide.
> > But there is a small bug I can't find out myself to make it run
> > properly. Can someone help? Thanks a lot.
> >
> > Jianhui
> > ##########################
> > set dcdFile n_aka3rm14w6_run10.dcd ;# name of your psf file
> >
> > set parm aka3rm14w6.prmtop ;# name of parm file
> >
> > set incrm 1
> > ##########################
> > mol load parm7 $parm dcd $dcdFile
> >
> > set num_steps [molinfo top get numframes]
> > puts $num_steps
> > set out [open helixcontent.dat w]
> >
> > for {set frme 1} {$frme <= $num_steps} {incr frme $incrm} {
> > puts $frme
> >
> > set hlxflag 0
> > set hlxcont 0
> >
> > ###### From resid 125 to 148 is amino acid.
> > for {set i 125} {$i <= 148 } { incr i} {
> > set atom [atomselect top "protein and name CA and resid $i"]
> > $atom frame $frme
> >
> > set phi [$atom get phi]
> > set psi [$atom get psi] if { $phi <= -30 && $phi >= -90
> > && $psi <= -17 && $psi >= -77 } {
> > if {$hlxflag == 0} {
> > set num 1
> > set hlxflag 1
> > } elseif {$hlxflag == 1} {
> > set num [expr $num + 1]
> > }
> > } else {
> > if {$hlxflag == 1} {
> > set hlxflag 0
> > if { $num > 2 } { set hlxcont [expr $num - 2]
> > }
> > }
> >
> > $atom delete
> > }
> > set cont [expr $hlxcont / 24]
> > puts $out "$frme $cont"
> > }
> > exit
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>