VMD-L Mailing List

From: Aitor Gonzalez (Aitor.Gonzalez_at_EMBL-Heidelberg.de)
Date: Fri Dec 08 2000 - 05:26:00 CST

Thank you for the help. I hope it works, because I don't know anything
about progrmming languages.

sincerely.

On Thu, 7 Dec 2000, John Stone wrote:

>
> Hi,
>
> On Thu, Dec 07, 2000 at 01:51:07PM +0100, Aitor Gonzalez wrote:
> > I have a serie of pdb models between a start and an end pdb file. Does
> > someone have a script to make it.
>
> I just wrote up a script which should do the trick for you, you will
> just need to use the right format string to make it work for your file
> naming conventions, two examples are included. Its a very simple script,
> but should work fine for your application. Let us know if you need
> more help with this.
>
> Enjoy,
> John Stone
> vmd_at_ks.uiuc.edu
>
> ##
> ## "animatepdbs" - A Tcl script to load a consecutively numbered
> ## sequence of PDB files.
> ##
> ## Parameters:
> ## start - "frame number" of first PDB file in sequence
> ## end - "frame number" of last PDB file in sqeuence
> ## format - a Tcl format string which describes the filename/numbering
> ## used.
> ##
> ## To load a sequence of PDB files named 0.pdb 1.pdb 2.pdb 3.pdb one
> ## would call this proc with: animatepdbs 0 3 "%d.pdb"
> ##
> ## To load a sequence of PDB files named as foo0000.pdb foo0001.pdb foo0002.pdb
> ## one would call this proc with: animatepdbs 0 2 "foo%04d.pdb"
> ##
>
> proc animatepdbs {start end fileformat} {
> set filename [format $fileformat [expr $start]]
> incr start
> puts "Reading initial frame in PDB sequence $filename"
> mol load pdb $filename
>
> puts "Reading PDB files as an animation..."
> for {set i $start} {$i <= $end} {incr i 1} {
> set filename [format $fileformat [expr $i]]
> animate read pdb $filename
> }
> }
>
>
>
>
> --
> 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
>