[Chimera-users] Problem in using BondRot

[amin at imtech.res.in]

Dear Dr. Pettersen and Dr. Meng, 

Thanks for the suggestion. I tried the simpler scripts and they work.
But I am not sure that what atoms are moved when I set res.phi =
-res.phi. The earlier script had set anchor residues to solve this
problem. Can you please guide me on how to use anchor residues on newer
versions of chimera? 

Warm Regards. 

Amin. 

On 2014-02-09 07:44, Eric Pettersen wrote: 

> Hi Amin, 
> As Elaine alluded to, the code for changing phi/psi is a lot simpler than what was necessary in 2005. In particular you can just assign a value to the phi or psi attribute to change it. Therefore in your script, the loop would just be: 
> 
> for res in mol.residues: 
> if res.phi is not None: 
> res.phi = -res.phi 
> 
> --Eric 
> 
> Eric Pettersen 
> UCSF Computer Graphics Lab 
> 
> 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 [1] . 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. 
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

 

Links:
------
[1]
http://plato.cgl.ucsf.edu/pipermail/chimera-users/2005-September/000456.html
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