VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Tue Dec 20 2016 - 07:35:02 CST

If you are interested in seeing the drawn components change with each frame
you need to slow down the loop. To do that you need to use the tcl command

after 1000

This will slow down the loop.

You also need to do

display update

in each loop iteration so that while the loop stops for the interval
specified with "after" the display is updates so you can "visualize" the
drawn component.

Hope this helps.

Best,
/A

On Dec 21, 2016 02:29, "Ajasja Ljubetič" <ajasja.ljubetic_at_gmail.com> wrote:

> Hi Amit,
>
> I guess, you would like to redraw he arrows after the frame changes.
> You can do this using TCL callbacks
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node159.html
>
> In particular see vmd_frame(molid).
>
> An example that draws the size of the unit cell for each frame is here
> http://www.ks.uiuc.edu/Research/vmd/script_library/
> scripts/pbcbox/pbcbox.tcl
>
> Best,
> Ajasja
>
>
> On 20 December 2016 at 13:41, Ashar Malik <asharjm_at_gmail.com> wrote:
>
>> since you are drawing a new thing every frame and don't need to see the
>> previous thing in the current selection - you should use
>>
>> draw delete all
>>
>> I think this should delete everything drawn and redraw at the new
>> positions you pass it - which I am guessing is coming from the loop.
>> (If you are drawing all this in a loop and deleting in the same iteration
>> - it might get drawn and deleted too fast -- ??? Not sure if that is what
>> you want ?? )
>> Hope this helps. Otherwise write back.
>>
>>
>> On Wed, Dec 21, 2016 at 1:28 AM, Amit Gupta <amit__at_outlook.in> wrote:
>>
>>> Hi,
>>>
>>> Yes I realized it and added it later on. Now I can see all the arrows,
>>> but together! I mean they are not changing with frame, rather all arrows
>>> from all frames are visible all the time
>>> ------------------------------
>>> *From:* Ashar Malik <asharjm_at_gmail.com>
>>> *Sent:* Tuesday, December 20, 2016 5:49:33 PM
>>> *To:* Amit Gupta
>>> *Cc:* vmd-l_at_ks.uiuc.edu
>>> *Subject:* Re: Fw: vmd-l: Draw arrows in trajectory file
>>>
>>> Hi,
>>>
>>> I think this maybe because you are not updating your selections
>>> properly. to see the arrow move - I guess your selections for arrows need
>>> to be updated on a frame by frame basis.
>>> Try either "$sel update" after "$sel frame $i"
>>>
>>> or drop the use of $sel update and use make selections like ...
>>>
>>> set end [lindex [[atomselect top "index $n_atom" frame $i] get {x y z}]
>>> 0]
>>>
>>> notice "frame $i" in the command you used. This will force a selection
>>> in the frame controlled by the loop.
>>> I think this should fix it. Otherwise - write back.
>>>
>>> Best,
>>> /A
>>>
>>> On Tue, Dec 20, 2016 at 10:45 PM, Amit Gupta <amit__at_outlook.in> wrote:
>>>
>>>>
>>>> Sorry I sent the message below to the person who replied rather than to
>>>> mailing list:
>>>>
>>>>
>>>> Thank you for the reply. I modified the script as written at the bottom
>>>> of mail and it worked fine (did not crash). However now i notice that
>>>> arrows are drawn only once, in the first frame. After which I do not see
>>>> any movement in the arrows. Is there any way to draw arrows per frame?
>>>>
>>>>
>>>>
>>>> Modified lines that worked:
>>>>
>>>> set end_temp [atomselect top "index $n_atom"]
>>>> set end [lindex [ $end_temp get {x y z}] 0]
>>>>
>>>> set start_temp [atomselect top "index $current_c_atom_index"]
>>>> set start [lindex [$start_temp get {x y z}] 0]
>>>>
>>>> $end_temp delete
>>>> $start_temp delete
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> From: Norman Geist <norman.geist_at_uni-greifswald.de>
>>>> Sent: Tuesday, December 20, 2016 2:07:25 PM
>>>> To: 'Amit Gupta'
>>>> Subject: AW: vmd-l: Draw arrows in trajectory file
>>>>
>>>>
>>>> You produced a common memory leak with many atomselects which you never
>>>> clear.
>>>> After you no more need an atomselect object, you should call “delete”
>>>> on it to free memory.
>>>>
>>>> Eg.:
>>>>
>>>> set a [atomselect top all]
>>>> set list [$a get index]
>>>> $a delete; #<-------
>>>>
>>>> So whats happening is that vmd gets killed for eating up all the memory.
>>>>
>>>> Best of luck
>>>>
>>>> Norman Geist
>>>>
>>>>
>>>>
>>>>
>>>> Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im
>>>> Auftrag von Amit Gupta
>>>> Gesendet: Dienstag, 20. Dezember 2016 07:31
>>>> An: vmd-l_at_ks.uiuc.edu
>>>> Betreff: vmd-l: Draw arrows in trajectory file
>>>>
>>>>
>>>> I want to draw come arrows in a lammps trajectory file, indicating
>>>> movement of certain vectors.
>>>> I have written script below, it works fine for single frame, but for
>>>> more than one frame, VMD crashes without any message (even in console). Can
>>>> anyone suggest a reason?
>>>>
>>>>
>>>> draw color yellow
>>>>
>>>> ##-----------Draw arrow subroutine from VMD website----------
>>>>
>>>>
>>>>
>>>> proc vmd_draw_arrow {mol start end} {
>>>>
>>>> # an arrow is made of a cylinder and a cone
>>>>
>>>> set middle [vecadd $start [vecscale 0.75 [vecsub $end $start]]]
>>>>
>>>> graphics $mol cylinder $start $middle radius 0.1
>>>>
>>>> graphics $mol cone $middle $end radius 0.3
>>>>
>>>> }
>>>>
>>>>
>>>>
>>>> ##----------------------------------------------------------
>>>> ----------------------
>>>>
>>>>
>>>>
>>>> set n [molinfo top get numframes]
>>>>
>>>> set sel [atomselect top "all"]
>>>>
>>>> set n_list [atomselect top "type 6"] #get indexes of all nitrogens in
>>>> molecules
>>>>
>>>> set all_n_atoms [$n_list get index]
>>>>
>>>>
>>>>
>>>> for {set i 0} {$i < $n} {incr i} {
>>>>
>>>> $sel frame $i
>>>>
>>>> foreach n_atom $all_n_atoms {
>>>>
>>>> set current_c_atom_index [expr $n_atom - 1] # get index of C
>>>> attached to N
>>>>
>>>> set end [lindex [[atomselect top "index $n_atom"] get {x y z}]
>>>> 0]
>>>>
>>>> set start [lindex [[atomselect top "index
>>>> $current_c_atom_index"] get {x y z}] 0]
>>>>
>>>> draw arrow $start $end
>>>>
>>>> }
>>>>
>>>> }
>>>>
>>>>
>>>> Sorry if certain logic seems slightly convoluted, still getting used to
>>>> TCL!
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Best,
>>> /A
>>>
>>
>>
>>
>> --
>> Best,
>> /A
>>
>
>