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From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jul 12 2011 - 15:17:50 CDT
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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.
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