From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Oct 26 2015 - 17:37:04 CDT

On Mon, Oct 26, 2015 at 6:25 PM, Aris Marcolongo <aris.marcolongo_at_gmail.com>
wrote:

> ????
>
> I have no access to my VMD version right now to test the new script... I
> noticed BY MYSELF that I was by mistake using an older version and I wanted
> to understand why the old version did not work in order to climb the tcl
> learning curve... I do not want to change the script, simply to understand
> how things work...
>

​you are not making much sense (to me). ​there are better ways to learn Tcl
than trying to understand why a piece of code may be broken, e.g. from
here: ​https://www.tcl.tk/man/tcl8.5/tutorial/tcltutorial.html

..and if you insist to find out what the problem was, ​then you should do
what every programmer does in such a case. use a tool that allows you to do
a side-by-side comparison, compare the two versions of the script, cross
reference with either the Tcl documentation or the VMD documentation (or
both) and draw your conclusions and try to understand. that you can only do
by yourself. you cannot expect people on this list or anywhere to do that
for you.

in any case, this is very different from your original inquiry where you
were indicating (rather drastically) that you were primarily interested in
getting a script/tool that works for the trajectory path plotting. well,
that question is answered and we can close the case now.

axel.

>
> Cheers,
>
> Aris
>
> 2015-10-26 23:10 GMT+01:00 Axel Kohlmeyer <akohlmey_at_gmail.com>:
>
>>
>>
>> On Mon, Oct 26, 2015 at 6:04 PM, Aris Marcolongo <
>> aris.marcolongo_at_gmail.com> wrote:
>>
>>> Hello,
>>>
>>> I just noticed that I was using a different source file than the
>>> one I linked before:
>>>
>>>
>>> http://www.ks.uiuc.edu/Research/vmd/old/script_library_old/trajectory_path/trajectory_path.vmd
>>>
>>> Maybe this can be the source of the problem? Actually in the old version
>>> there is this command:
>>>
>>
>> ​it is pointless to speculate about such matters, and even more pointless
>> to try making a superseded version of a script work for no good reason.
>> don't you think that there may have been a good reason that the "old"
>> version was replaced by a newer one? doesn't your alarm bell ring, if you
>> have an URL that has the word "old" in it *twice*??
>>
>> i've just tested the code from the "proper" URL and it works as
>> advertised. what else do you want?
>>
>> axel.
>> ​
>>
>>
>>
>>>
>>> mol new graphics [$selection text]
>>>
>>> which is not present in the new version....
>>>
>>> 2015-10-26 21:39 GMT+01:00 Axel Kohlmeyer <akohlmey_at_gmail.com>:
>>>
>>>>
>>>>
>>>> On Mon, Oct 26, 2015 at 4:06 PM, Aris Marcolongo <
>>>> aris.marcolongo_at_gmail.com> wrote:
>>>>
>>>>> No clue? Is there an other simple way to leave the track of the motion
>>>>> of selected atoms using VMD?
>>>>>
>>>>
>>>> ​the script you are pointing to works as documented​, but the command
>>>> it defines is called "trajectory_path" and not "traj".
>>>> the error message you quote does not make sense with the script you
>>>> quoted. it cannot generate this error.
>>>>
>>>> PEBCAC?
>>>>
>>>> axel.
>>>>
>>>>
>>>>
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Aris
>>>>>
>>>>>
>>>>> 2015-10-26 12:02 GMT+01:00 Aris Marcolongo <aris.marcolongo_at_gmail.com>
>>>>> :
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> I am trying to use this script:
>>>>>>
>>>>>>
>>>>>> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/trajectory_path/ <https://ewa.epfl.ch/owa/redir.aspx?SURL=-XIwpi3phwsVq54Qgbd-NJ_5lkgmK5aQGTkckEriak_bdi6o9N3SCGgAdAB0AHAAOgAvAC8AdwB3AHcALgBrAHMALgB1AGkAdQBjAC4AZQBkAHUALwBSAGUAcwBlAGEAcgBjAGgALwB2AG0AZAAvAHMAYwByAGkAcAB0AF8AbABpAGIAcgBhAHIAeQAvAHMAYwByAGkAcAB0AHMALwB0AHIAYQBqAGUAYwB0AG8AcgB5AF8AcABhAHQAaAAvAA..&URL=http%3a%2f%2fwww.ks.uiuc.edu%2fResearch%2fvmd%2fscript_library%2fscripts%2ftrajectory_path%2f>
>>>>>>
>>>>>>
>>>>>> for visualizing the trajectory of a single atom with VMD,
>>>>>> here with index 59. I am a beginner with VMD, and I just wrote in
>>>>>> the TkC console:
>>>>>>
>>>>>> > source traj.tcl
>>>>>> > set crystal [atomselect top "index 59"]
>>>>>> atomselect11
>>>>>> > traj $crystal scale
>>>>>>
>>>>>> but I finally end up with the error.
>>>>>>
>>>>>> Illegal molecule specification 'index 59': Could not
>>>>>> find molecule 'index 59'. mol new operates on one molecule only
>>>>>>
>>>>>> How can I solve this problem?
>>>>>>
>>>>>>
>>>>>> Thanks a lot for any help,
>>>>>>
>>>>>>
>>>>>> Aris
>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>>>> College of Science & Technology, Temple University, Philadelphia PA, USA
>>>> International Centre for Theoretical Physics, Trieste. Italy.
>>>>
>>>
>>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>>
>
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.