VMD-L Mailing List

From: Aris Marcolongo (aris.marcolongo_at_gmail.com)
Date: Mon Oct 26 2015 - 17:42:25 CDT

Ok, thanks for the link !

2015-10-26 23:37 GMT+01:00 Axel Kohlmeyer <akohlmey_at_gmail.com>:

>
>
> 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 pointless to try making a superseded version of a script work for no good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.
>