VMD-L Mailing List

From: Fahimeh Baftizadeh (fahimeh.baftizadeh_at_googlemail.com)
Date: Wed Feb 27 2013 - 10:19:02 CST

Thanks, You are right. I tried to used the "user field" but I can not yet
update the color each frame, here is my script which I found and modified
it a bit:

proc pdbbfactor { fname } {
  mol new $fname waitfor all
  set all [atomselect top all]
  set frame 0
  set in [open $fname r]
  set beta {}
  while { [gets $in line] != -1 } {
    switch -- [string range $line 0 3] {
      END {
        $all frame $frame
        $all set user $beta
        set beta {}
        incr frame
      }
      ATOM -
      HETA {
        lappend beta [string range $line 61 66]
      }
    }
  }
}

pdbbfactor new.pdb

set molid 0

mol colupdate 0 $molid on

mol scaleminmax 0 $molid 0.0 2.0

animate goto start

Fahimeh

On Tue, Feb 26, 2013 at 2:12 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> You need to make sure to delete your atom selections.
> In your do_refresh_occupency proc, you are creating selections
> within a doubly nested loop, but they are never getting deleted...
> That's the first thing that you would need to fix there if you were
> going to do it this way. Even that would be a bad idea however.
> It is far more efficient to set _all_ of the occupency values with
> a single atom selection operation, e.g.:
>
> replace this operation in your reader loop:
> set occu($i) [lindex $line 8]
>
> with something like this:
> lappend occlist [lindex $line 8]
>
> Then, in do_refresh_occupancy, you could get rid of the innermost loop
> and do something more like this:
> set s [atomselect $molid all]
> $s set occupancy $occlist
>
> That would be massively faster than what you are doing presently.
>
> There are yet other ways of doing this...
>
> If you want to store occupancy per-frame, you probably want to store it
> to one of the "user" fields rather than occupancy, and then VMD will
> automatically update it as you animate the trajectory all by itself.
> See the various VMD tutorials to learn how to use these features.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Feb 26, 2013 at 01:42:59PM -0500, Fahimeh Baftizadeh wrote:
> > Hello,
> > I am trying to load a pdb trajectory and update the occupancy column
> at
> > each fram. As far as I know, this is not automatic in VMD and I had to
> > write a tcl script for that. Here is my script:
> > mol new {new2.pdb} type pdb waitfor all
> > set molid 0
> > set i 0
> > set pattern {ATOM}
> > set fp [open "new2.pdb" r]
> > while {[gets $fp line] !=-1} {
> > if {[regexp $pattern $line]} {
> > set occu($i) [lindex $line 8]
> > incr i}
> > }
> > close $fp
> > proc do_refresh_occupancy {args} {
> > global occu molid
> > set a [molinfo $molid get numatoms]
> > set f [molinfo $molid get frame]
> > for {set j 0} {$j <= $f} {incr j} {
> > for {set i 0} {$i < $a} {incr i} {
> > set s [atomselect $molid "index $i"]
> > $s set occupancy $occu([expr $a*$j+$i])
> > }
> > }
> > }
> > trace variable vmd_frame($molid) w do_refresh_occupancy
> > mol colupdate 0 $molid on
> > mol scaleminmax 0 $molid 0.0 2.0
> > animate goto start
> > do_refresh_occupancy
> > in which I read and load new2.pdb ... saving the occupancy column and
> then
> > update it each fram. This is maybe complicated one but I am new to
> tcl and
> > didn't know how to make it simpler.
> > My problem now is that if new2.pdb is large ... then VMD crash and
> > complain for memory ... (malloc)
> > Could you please help me to solve this problem?
> > Thanks
> > Fahimeh
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
> 

-- 
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"If you torture the data long enough, they will confess to anything!" John
Tukey