[Chimera-users] selection of specific bonds

[Damien Larivière]

Dear Elaine and Eric,

That worked quite fine. Many thanks for your help on this.

My best regards,

Damien

Le 11/12/2019 à 19:25, Eric Pettersen a écrit :
> … and if you want to find the carbonyls only in GLU residues, you 
> would intersect the specifier with :GLU, /i.e./:
>
> select carbonyl & :glu
>
> —Eric
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
>
>> On Dec 11, 2019, at 9:34 AM, Elaine Meng <meng at cgl.ucsf.edu 
>> <mailto:meng at cgl.ucsf.edu>> wrote:
>>
>> Hi Damien,
>> You’ll like this… simply the command:  select carbonyl
>>
>> It selects the atoms as well as the bond between them.
>>
>> You can specify in the command line any of the functional groups that 
>> appear in the menu under Select… Chemistry… functional group.  It’s 
>> mentioned here:
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#builtin>
>>
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>>> On Dec 11, 2019, at 8:02 AM, Damien Larivière 
>>> <damien at fourmentinguilbert.org 
>>> <mailto:damien at fourmentinguilbert.org>> wrote:
>>>
>>> Dear All,
>>>
>>> My question is naive but I have difficulties to figure out how to do 
>>> it with Chimera.
>>>
>>> I would like to select specifically the group of two atoms (C and O) 
>>> formed in a carbonyl bond C=O for all, say, GLU residues of a protein.
>>>
>>> Is there a way, via a command line, to do it?
>>>
>>> Thanks for your help on this.
>>>
>>> Damien
>>
>>
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