From: Francesca Lønstad Bleken (FrancescaL.Bleken_at_sintef.no)
Date: Fri Oct 14 2016 - 10:58:01 CDT

Thank you very much for your quick and good answers.

Francesca

> Il giorno 14 ott 2016, alle ore 17:05, John Stone <johns_at_ks.uiuc.edu> ha scritto:
>
> Hi,
> It wasn't clear to me if in Francesca's case she was modifying bonds
> prior to the selection. So long as the VMD structure analysis is
> up-to-date at the time the selection is done (e.g. if one would change
> any bonds interactively or the like, you would have to do a "mol reanalyze"),
> then the "fragment" selection Axel suggests would be faster than the
> "withinbonds" suggestion I gave earlier. The "withinbonds" selection
> has to walk the bondlist during selection, whereas "fragment" does not,
> so "fragment" would be much faster if you're not modifying anything in the
> structure.
>
> Cheers,
> John
>
>> On Fri, Oct 14, 2016 at 10:52:54AM -0400, Axel Kohlmeyer wrote:
>> On Fri, Oct 14, 2016 at 6:39 AM, Francesca Lønstad Bleken
>> <FrancescaL.Bleken_at_sintef.no> wrote:
>>> Hi,
>>>
>>>
>>>
>>> Is there a way to select atoms according to bonding in the sense "select a
>>> molecule"
>>
>> you can select by the "fragment" property, which is generated by VMD
>> based on connectivity.
>>
>> axel.
>>
>>
>>>
>>>
>>>
>>> I have used topotools to clear and guess new bonds, and visually this look
>>> ok, but I would like to select one and one molecule.
>>>
>>> With getbonds I can get the list of all bonds, but since the system is big I
>>> would like to know if there are any solutions or suggestions for how to
>>> select just one of the "new" molecules.
>>>
>>>
>>>
>>> Best regards,
>>>
>>> Francesca
>>>
>>>
>>
>>
>>
>> --
>> 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.
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/