[Chimera-users] Problem in using BondRot

[amin at imtech.res.in]

Thanks Dr. Pettersen. This helped me figure out most of the things. The
last problem I had was with rotation of prolines. I found this thread
regarding the problem
http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-November/006938.html
which I hope will solve everything. Thanks for the help. 

Amin. 

On 2014-02-12 06:42, Eric Pettersen wrote: 

> I guess I didn't completely answer your question. If you want strict control over which side of the phi/psi moves, then you are going to have to set up the bond rotation yourself rather than use res.phi/res/psi. You do this by finding the bond you want to rotate and then using the BondRotMgr module: 
> 
> from BondRotMgr import bondRotMgr 
> rot = bondRotMgr.rotationForBond(bond) 
> rot.anchorSide = anchor_atom 
> 
> then you'll have to measure the current phi/psi (which you could get via res.phi/res.psi) and use: 
> 
> rot.increment(angle_diff) 
> 
> to get to the desired value. When you are completely done adjusting the bond rotation, call: 
> 
> rot.destroy() 
> 
> --Eric 
> 
> On Feb 11, 2014, at 4:57 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote: 
> 
> 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 [1]
> 
> 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 [2] . 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
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