VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Oct 26 2015 - 17:10:41 CDT
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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to try making a superseded version of a script work for no good reason.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.
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