[Chimera-users] Fwd: Re: Question about selection...

[Yasser Almeida Hernández]

It works!!!
Thanks a lot, ;)



-------- Original Message --------
Subject: 	Re: [Chimera-users] Question about selection...
Date: 	Tue, 10 Aug 2010 13:49:55 -0500
From: 	Elaine Meng <meng at cgl.ucsf.edu>
Reply-To: 	Chimera BB <chimera-users at cgl.ucsf.edu>
To: 	Yasser Almeida Hernandez <almeida at cim.sld.cu>
CC: 	Chimera BB <chimera-users at cgl.ucsf.edu>



Hi Yasser,
if you want to generally select all singleton atoms (atoms not bonded  
to other atoms), you could use this command:

sel @/!bonds

this is an example of specification by attribute, described here:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descriptors>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 10, 2010, at 7:49 AM, Yasser Almeida Hernández wrote:

>  Hi...
>  The problem is that I have hundreds of pdb files with this format:  
> four models (or less), where each one is an aminoacid and a single  
> atom. Mostly, the single atom is an heteroatom and i select it with  
> :/isHet, but sometimes this atom is a protein atom with the ATOM  
> field and then, the :/isHet selection doesn't work...
>  There is some tricky way to select this single atom types (ATOM),  
> according to the structure of the pdb file...???
>  Thanks

.




----- Terminar mensaje reenviado -----


-- 
Yasser Almeida Hernández, BSc
Center of Molecular Inmunology (CIM)
Nanobiology Group
P.O.Box 16040, Havana, Cuba
Phone: (537) 214-3178
almeida at cim.sld.cu

----------------------------------------------------------------
Correo FENHI


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-------- Original Message --------
Subject: 	Re: [Chimera-users] Question about selection...
Date: 	Tue, 10 Aug 2010 13:49:55 -0500
From: 	Elaine Meng <meng at cgl.ucsf.edu>
Reply-To: 	Chimera BB <chimera-users at cgl.ucsf.edu>
To: 	Yasser Almeida Hernandez <almeida at cim.sld.cu>
CC: 	Chimera BB <chimera-users at cgl.ucsf.edu>



Hi Yasser,
if you want to generally select all singleton atoms (atoms not bonded to other atoms), you could use this command:

sel @/!bonds

this is an example of specification by attribute, described here:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descriptors>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 10, 2010, at 7:49 AM, Yasser Almeida Hernández wrote:

>  Hi...
>  The problem is that I have hundreds of pdb files with this format: four models (or less), where each one is an aminoacid and a single atom. Mostly, the single atom is an heteroatom and i select it with :/isHet, but sometimes this atom is a protein atom with the ATOM field and then, the :/isHet selection doesn't work...
>  There is some tricky way to select this single atom types (ATOM), according to the structure of the pdb file...???
>  Thanks

.


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