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@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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