[Chimera-users] Problem in using BondRot

[Eric Pettersen]

Hi Amin,
	I'm not sure why you care which side moves, but by default the "smaller" side moves.  So if the residue is near the N terminus then the N-terminal part will move, if it's near the C terminus then the C-terminal side will move.  Unless these changes are relative to some other structure, it shouldn't matter which side "moves"; the resulting conformation is the same either way.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu


On Feb 8, 2014, at 8:33 PM, amin wrote:

> 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 . 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
>  
>  

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