VMD-L Mailing List

From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Wed Jul 13 2011 - 08:29:18 CDT

(sorry, I sent the message to axel's private email by mistake)

Argh. I feel stupid. Of course simply sourcing works. Here is what worked
for me:

# load in molecule and trajectory and then:

proc do_source {args} {

    set molid 0
    # get the current frame number
    set frame [molinfo $molid get frame]
    source outputhole_$frame.vmd_plot
}

trace variable vmd_frame(0) w do_source
animate goto 0

On Tue, Jul 12, 2011 at 10:17 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Tue, Jul 12, 2011 at 3:19 PM, maria goranovic
> <mariagoranovic_at_gmail.com> wrote:
> > Hi John
> > Thank you for the answers. I understand most of it.
> > I am trying to source in a file containing a new set of draw directives
> on
> > each frame, hence source alone does not work, which is why I was trying
> to
>
> why should source not work. if you have one file per frame,
> you can just source the file for that frame.
>
> another option would be to store the contents of the files
> in tcl lists and then use the tcl eval command.
>
> > understand Axel's script.
> > It is still not clear to me what function (equivalent of do_dipframe) I
> > should call to "attach" the file to each frame ?
>
> you can use any function you want.
> the trace command will execute the
> registered function any time a certain
> condition is met, in this case it will be
> called when the frame number is updated.
>
> cheers,
> axel.
>
> > On Tue, Jul 12, 2011 at 8:19 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> >>
> >> Hi,
> >> I'll give you a few more tips on the questions you had below:
> >>
> >> On Mon, Jul 11, 2011 at 11:12:11AM +0200, maria goranovic wrote:
> >> > Hi Axel,
> >> > Thank you for the help. Appreciate it. I have 4 questions, if you
> do
> >> > not
> >> > mind?
> >> > 1. In your example, you use the procedure do_dipdraw to execute a
> >> > command
> >> > (vmd_draw_vector). In my case, I just need to read in the contents
> of
> >> > a
> >> > file. So the procedure do_dipdraw should be replaced by a function
> >> > which
> >> > reads in the entire file containing the draw commands. How do I do
> >> > this?
> >>
> >> I haven't been following this thread so I'm not entirely sure what
> you're
> >> trying to do, but if you have a file that contains a bunch of drawing
> >> commands,
> >> you can simply execute the file like this:
> >> source filename.tcl
> >> or
> >> play filename.tcl
> >>
> >> The "source" command processes all of the commands in the file at once.
> >> The "play" command reads the file a line-at-a-time, and processes the
> >> commands on each line, causing display updates etc after each command.
> >> Generally it is best to use "source" unless you have a specific reason
> >> to use "play" instead.
> >>
> >> > 2. I also cannot really understand the need of following lines of
> >> > your
> >> > script?*
> >>
> >> I added comments below.
> >>
> >> > # if there is information in the dipdate ($frame) list element
> >> > if {[info exists dipdata($frame)]} then {
> >>
> >> This line checks to see if the Tcl array contains data for the active
> >> frame...
> >>
> >> > # if $dipgraph has some value
> >> > if {[info exists dipgraph]} then {
> >>
> >> This line is checking to see if there is a "dipgraph" variable or not.
> >>
> >> > # delete all elements of $dipgraph? Why?
> >> > foreach g $dipgraph {
> >> > graphics $molid delete $g
> >> > }
> >>
> >> I assume this is deleting all of the old graphics objects, so that
> >> they can be redrawn on the next frame, without leaving the old objects
> >> from the previous frame displayed on the screen.
> >>
> >> > }
> >>
> >>
> >> > 3. I tried something like this, but run into problems. VMD seems
> >> > unable to
> >> > exit from the for loop where the files are read and assigned to a
> >> > variable
> >> > $lines($frame). Why does this happen? Am I not reading the file
> >> > correctly?
> >>
> >> I believe your loop is not incrementing "i", but instead it is trying
> >> to increment "$i", which is most likely the source of your problem.
> >> You can save yourself a lot of trouble when debugging problems like this
> >> by adding a "puts" call within the loop and printing out the loop
> >> iteration, and/or any other information that is useful to determine
> >> what is happening in your code.
> >>
> >> > ########################
> >> > mol load gro protein.gro
> >> > mol addfile {protein.xtc} type {xtc} first 0 last 5 step 1 waitfor
> >> > all
> >> > #proc readdata {} {
> >> > #What goes here??
> >> > #}
> >> > # read in files to be appended to each frame
> >> > set n [molinfo 0 get numframes]
> >> > # I think this is what you meant by : "you can just do a per frame
> >> > open/close and read in the file" ?
> >> > for {set i 0} {$i<$n} {incr $i} {
> >> > set dat [open "outputhole_$i.vmd_plot" r]
> >> > set lines($i) *[gets $dat]
> >> > close $dat
> >> > }
> >> > puts $lines(0)
> >> > ########################
> >> > 4. Each file that I am trying to read for each frame has about
> 27000
> >> > draw
> >> > directives. I have about 100 frames. So can VMD easily handle
> >> > 100*27000
> >> > lines in an array variable without choking on memory?*
> >>
> >> VMD has no particular limits, it is only a question of the machine
> you're
> >> using and whether you're running a 32-bit or 64-bit version of VMD.
> >>
> >> Cheers,
> >> John Stone
> >> vmd_at_ks.uiuc.edu
> >>
> >> > Thank you for the help
> >> > Maria
> >> > On Fri, Jul 8, 2011 at 6:20 PM, Axel Kohlmeyer <akohlmey_at_gmail.com
> >
> >> > wrote:
> >> >
> >> > On Fri, Jul 8, 2011 at 10:56 AM, maria goranovic
> >> > <mariagoranovic_at_gmail.com> wrote:
> >> > > Hi Axel
> >> > > Thank you for the help. However, I am not much of an expert in
> >> > tcl or
> >> > vmd
> >> > > scripting and am learning. Hopefully I can please get some
> help?
> >> >
> >> > i can try.
> >> > > One difference between your setup and mine seems to be that in
> >> > your
> >> > setup
> >> > > all the data over frames which you are trying to import is
> lying
> >> > in
> >> > one
> >> > > file, and you read the file one at a time?
> >> >
> >> > i read the data up front and store it away in an array that is
> >> > indexed
> >> > by the frame number, since that is faster.
> >> > for the example of a dipole, there is not much data to store.
> >> > > So, here: each line is being read from zundel.dip and assigned
> to
> >> > the
> >> > > dipdata($i) array.
> >> >
> >> > exactly.
> >> > > for {set i 0} {$i < $n} {incr i} {
> >> > > # advance selection to the current frame and update.
> >> > > $sel frame $n
> >> > > $sel update
> >> > > set dipdata($i) [list [center_of_mass $sel] [gets $dip]]
> >> > > }
> >> > > close $dip
> >> >
> >> > > However, the data I need to read in each frame is not one line,
> >> > but an
> >> > > entire file.
> >> >
> >> > that doesn't make a difference. you can just do a per frame
> >> > open/close and read in the file. however, you can also stick
> >> > to the reading a file. the latter is just taking more time.
> >> > > Secondly, I did not really understand what seems to be the key
> >> > command:
> >> > > trace variable vmd_frame(0) w do_dipdraw
> >> >
> >> > > This means that the command do_dipdraw will be executed if
> >> > vmd_frame(0) is
> >> > > executed? what is the w for? what is vmd_frame(0) ?
> >> >
> >> > not executed but written to. vmd_frame is an array that records
> the
> >> > current frame number of each molecule. thus $vmd_frame(0) will
> give
> >> > you the current frame number for molecule 0. this array/variable
> >> > will
> >> > be updated by VMD whenever a new frame becomes current, and
> >> > then the "trace" will be triggered and do_dipdraw is launched.
> >> >
> >> > HTH,
> >> > * axel.
> >> >
> >> > > Thank you again,
> >> > > Maria
> >> > > On Fri, Jul 8, 2011 at 3:31 PM, Axel Kohlmeyer
> >> > <akohlmey_at_gmail.com>
> >> > wrote:
> >> > >>
> >> > >> On Fri, Jul 8, 2011 at 8:59 AM, maria goranovic
> >> > >> <mariagoranovic_at_gmail.com> wrote:
> >> > >> > Hi
> >> > >> > I have a trajectory, and I want to source in a different
> >> > draw-command
> >> > >> > containing file on each frame. The files to be sourced in
> >> > contain
> >> > >> > several
> >> > >> > draw commands as below:
> >> > >> > ...
> >> > >> > draw point { * 67.340 * 84.391 * 32.398}
> >> > >> > draw point { * 67.340 * 84.391 * 32.340}
> >> > >> > draw point { * 67.340 * 84.410 * 32.284}
> >> > >> > draw point { * 67.340 * 84.446 * 32.238}
> >> > >> > draw point { * 67.340 * 84.495 * 32.206}
> >> > >> > draw point { * 67.340 * 84.552 * 32.192}
> >> > >> > draw point { * 67.340 * 84.611 * 32.196}
> >> > >> > draw point { * 67.340 * 84.664 * 32.220}
> >> > >> > draw point { * 67.340 * 84.707 * 32.260}
> >> > >> > draw point { * 67.340 * 84.735 * 32.311}
> >> > >> > draw point { * 67.353 * 84.567 * 32.605}
> >> > >> > ...
> >> > >> >
> >> > >> > the idea is to view the trajectory and draw a new set of
> >> > points
> >> > each
> >> > >> > frame.
> >> > >> > Can someone please suggest how to accomplish this?
> >> > >> > I tried something like the following to load 5 frames from a
> >> > 125-frame
> >> > >> > trajectory. The files temp_$j.vmd_plot contain data like the
> >> > above.
> >> > The
> >> > >> > script below works, except that only the last set of points
> >> > i.e.
> >> > >> > outputhole_5.vmd_plot are displayed, and no others. When I
> >> > look
> >> > back
> >> > >> > into
> >> > >> > the trajectory, VMD has lost information of previous
> >> > temp_$j.vmd_plot
> >> > >> > files.
> >> > >> > How do I keep the data in the display?
> >> > >>
> >> > >> that is not how this will work.
> >> > >>
> >> > >> have a look at item 5.2 in this document.
> >> > >>
> >> > >>
> >> > >>
> >> >
> >> >
> http://sites.google.com/site/akohlmey/redirect/cpmd-vmd.pdf?attredirects=0&d=1
> >> > >>
> >> > >> cheers,
> >> > >> * *axel.
> >> > >>
> >> > >>
> >> > >> > ====================
> >> > >> > mol load gro protein-aligned-50ns.gro
> >> > >> > # Load trajectory
> >> > >> > for {set j 0} {$j < 5 } {incr j} {
> >> > >> > # i goes like 1, 26, 51 ...
> >> > >> > set i [expr ($j*25)+1]
> >> > >> > # k goes like 25, 50, 75 ...
> >> > >> > set k [expr ($j+1)*25]
> >> > >> > mol addfile {protein-aligned.xtc} type {xtc} first $i last
> $k
> >> > step
> >> > 25
> >> > >> > waitfor 1 0
> >> > >> > # this file contains the draw statements
> >> > >> > source temp_$j.vmd_plot
> >> > >> > }
> >> > >> > ========================
> >> > >> >
> >> > >> > --
> >> > >> > Maria G.
> >> > >> > Technical University of Denmark
> >> > >> > Copenhagen
> >> > >> >
> >> > >>
> >> > >>
> >> > >>
> >> > >> --
> >> > >> Dr. Axel Kohlmeyer
> >> > >> akohlmey_at_gmail.com *http://goo.gl/1wk0
> >> > >>
> >> > >> Institute for Computational Molecular Science
> >> > >> Temple University, Philadelphia PA, USA.
> >> > >
> >> > >
> >> > >
> >> > > --
> >> > > Maria G.
> >> > > Technical University of Denmark
> >> > > Copenhagen
> >> > >
> >> >
> >> > --
> >> > Dr. Axel Kohlmeyer
> >> > akohlmey_at_gmail.com *http://goo.gl/1wk0
> >> >
> >> > Institute for Computational Molecular Science
> >> > Temple University, Philadelphia PA, USA.
> >> >
> >> > --
> >> > Maria G.
> >> > Technical University of Denmark
> >> > Copenhagen
> >>
> >> --
> >> NIH Resource 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
> >
> >
> >
> > --
> > Maria G.
> > Technical University of Denmark
> > Copenhagen
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
> 

-- 
Maria G.
Technical University of Denmark
Copenhagen