VMD-L Mailing List

From: Aris Marcolongo (aris.marcolongo_at_gmail.com)
Date: Mon Oct 26 2015 - 17:25:40 CDT

????

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...

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 to try making a superseded version of a script work for no good reason.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