VMD-L Mailing List

From: M K (mahyar.karimi20_at_gmail.com)
Date: Wed Oct 14 2015 - 21:12:05 CDT

Thank you so much again!
Both methods worked perfectly :)

On Thu, Oct 15, 2015 at 12:53 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> or you can just delete the low-level graphics commands from the saved
> state file. that may be even more convenient.
>
> On Wed, Oct 14, 2015 at 9:52 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
>
>>
>>
>> On Wed, Oct 14, 2015 at 9:44 PM, M K <mahyar.karimi20_at_gmail.com> wrote:
>>
>>> Thank you so much. I tried it:
>>> It works when I load a normal trajectory file and add the box. However,
>>> it does not work when the trajectory has been loaded by "Load Visualization
>>> State" ...
>>>
>>
>> ​yes, because pbctools can only delete (specific) graphics elements, when
>> it had written them itself (and thus kept track of them).
>> when you load the visualization state, it is some low-level code in VMD
>> that restores the graphics elements, so you also have to use a low-level
>> graphics script command to delete those graphics elements. there is a
>> "graphics <molid> delete ​all option that allows to do this for
>> "everything".
>>
>> for details, please see the VMD users guide:
>> http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.2/ug/node129.html
>>
>> axel.
>>
>>
>>
>>
>>>
>>> On Fri, Sep 18, 2015 at 1:46 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
>>> wrote:
>>>
>>>>
>>>>
>>>> On Thu, Sep 17, 2015 at 11:22 PM, M K <mahyar.karimi20_at_gmail.com>
>>>> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I have drawn the box using pbc tool:
>>>>>
>>>>> pbc box -color white
>>>>>
>>>>> But I need to remove it now. Is there any command to delete it? Or I
>>>>> should load the whole trajectories from the beginning?
>>>>>
>>>>
>>>> http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
>>>>
>>>> ​how about: pbc box -off​
>>>>
>>>> ​axel.​
>>>>
>>>>>
>>>>> Thank you.
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> 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.
>