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@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

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@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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