[Chimera-users] Dummy atoms

[Jean Didier Pie Marechal]

Dear all,

I think the question was already posted but I can't find it.
I would like to make an atom I placed as an helium to a Dummy: What is the corresponding atom type in Chimera?

All the best
JD



Dr. Jean-Didier Maréchal
Professor Lector
Unitat de Química Física
Departament de Química
Universitat Autònoma de Barcelona
Edifici C.n.
08193 Cerdanyola (Barcelona)
Tel: +34.935814936
e-mail: JeanDidier.Marechal at uab.es

----- Missatge original -----
De: chimera-users-request at cgl.ucsf.edu
Data: Dimarts, Juny 24, 2008 9:00 pm
Assumpte: Chimera-users Digest, Vol 62, Issue 21

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> Today's Topics:
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>   1. Re: how could u know the order of atoms? (Eric Pettersen)
> 
> 
> --------------------------------------------------------------------
> --
> 
> Message: 1
> Date: Mon, 23 Jun 2008 14:22:31 -0700
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] how could u know the order of atoms?
> To: Kamal Al Nasr <k_alnasr at yahoo.com>
> Cc: chimera-users at cgl.ucsf.edu
> Message-ID: <8901DE4E-D117-4B18-968B-D3095AD735D4 at cgl.ucsf.edu>
> Content-Type: text/plain; charset="us-ascii"
> 
> On Jun 19, 2008, at 10:08 AM, Kamal Al Nasr wrote:
> 
> > Dear Sir/Madam,
> >
> > I am using Chimera viewer..and it is a great viewer ever...
> 
> Thanks!  I'm glad you like it.
> 
> >  I kindly have a question... how could you know (from PDB file) 
> the  
> > coorect bonding between atoms? I mean that how could you know 
> that  
> > this atom is connected with CA not N nor C.....do u have all 
> these  
> > bonds stored already in a database? or you use atom positions to  
> > determine that?
> 
> For standard amino and nucleic acids, Chimera has templates  
> containing the correct connectivity.  For non-standard residues it  
> bases the connectivity on inter-atomic distances, with a few added  
> heuristics (e.g. hydrogens can only have one bond).
> 
> The templates are accessible in the Python layer with the  
> chimera.restmplFindResidue() function.  You can look in the 
> Rotamers  
> extension for examples of its use.  The distance-based connectivity 
> 
> function is also available for an entire molecule as  
> chimera.connectMolecule().  It takes the molecule as its only  
> argument and adds bonds to it.
> 
> --Eric
> 
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
> 
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