[Chimera-users] Problem in using BondRot

Elaine Meng meng at cgl.ucsf.edu
Sat Feb 8 12:36:13 PST 2014


Hi Amin,
That is a pretty old message; probably the name of something changed ... it may be simpler now (in later versions of Chimera) that peptide residues are automatically assigned attributes named "phi" and "psi" with the torsion values.  If your script can get the current residue attribute value and multiply it by -1, it can then reset it to the new value.  I can't advise on python, but you can use the Chimera setattr command to specify the value of some attribute directly, for example to set phi to -60 for residue 40 in chain A:

setattr r phi -60 :40.a

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>

Best,
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 Feb 8, 2014, at 11:03 AM, amin at imtech.res.in wrote:

> Dear Chimera users,
> 
> I am trying to write a script to change the phi and psi angle of a peptide. I am trying to adapt the code from http://plato.cgl.ucsf.edu/pipermail/chimera-users/2005-September/000456.html . I am trying to invert the angles so I am multiplying the angles by -1. My code is 
> 
> import chimera
> 
> from chimera import selection, UserError, BondRot, replyobj
> 
> opened = chimera.openModels.open('fun.pdb')
> mol = opened[0]
> RES_LIST = mol.residues
> for res in mol.residues:
>       b = str(res.phi)
>       if b != 'None':
>            c = -1*float(b) 
>            atomsMap = res.atomsMap
>            N = atomsMap['N'][0]
>            CA = atomsMap['CA'][0]
>            C = atomsMap['C'][0]
>            CAmap = CA.bondsMap
>            phiBond = CAmap[N]
>            psiBond = CAmap[C]
>            phiAnchor = N
>            psiAnchor = CA
>            phi = BondRot(phiBond)
>            phi.setAngle(c, phiAnchor)
> 
> When I run this script i get the error 
> 
> phi.setAngle(c, phiAnchor)
> AttributeError: '_molecule.BondRot' object has no attribute 'setAngle'
> 
>  
> Can someone please help me with this?
> 
> Warm regards.
> 
> Amin.
> 




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