Thank you for your help! From testing on a few noodly structures, the function now behaves as intended. The link to the updated script is here in case any one wants to play around with the function: <https://github.com/delnatan/colabfold_chunker_utils/blob/9a697691b9a2c4da137f1c0d2c013ab9e02da832/straighten.py> [colabfold_chunker_utils.png] colabfold_chunker_utils/straighten.py at 9a697691b9a2c4da137f1c0d2c013ab9e02da832 · delnatan/colabfold_chunker_utils<https://github.com/delnatan/colabfold_chunker_utils/blob/9a697691b9a2c4da137f1c0d2c013ab9e02da832/straighten.py> github.com<https://github.com/delnatan/colabfold_chunker_utils/blob/9a697691b9a2c4da137f1c0d2c013ab9e02da832/straighten.py> I implemented the logic of for moving either N or C-term. like this: ``` for i, res in enumerate(mobile_sel): # find backbone C-alpha atom = res.find_atom("CA") # list containing 'small side' atom w.r.t C-alpha small_side_atoms = [] # handle proline differently (for now) if res.name != "PRO": for nb, bond in zip(atom.neighbors, atom.bonds): if nb.name == "N": small_side_atoms.append(bond.smaller_side.name) elif nb.name == "C": small_side_atoms.append(bond.smaller_side.name) # if we want to move the 'N' terminus if mobile_terminal == "N": # residue is near N-term (phi & psi is the smaller side) move_smaller = set(small_side_atoms) == {"N", "CA"} elif mobile_terminal == "C": # residue is near C-term (phi & psi is the smaller side) move_smaller = set(small_side_atoms) == {"CA", "C"} psi_assgn = random.normalvariate(mu=135.0, sigma=noise) res.set_psi(psi_assgn, move_smaller_side=move_smaller) phi_assgn = random.normalvariate(mu=-139.0, sigma=noise) res.set_phi(phi_assgn, move_smaller_side=move_smaller) ``` Thanks Eric and Elaine! -Daniel On Dec 19, 2024, at 5:17 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote: Hi Daniel, Your code looks good to me except that, as Elaine pointed out, you have phi and psi inverted. —Eric On Dec 19, 2024, at 3:51 PM, Daniel Elnatan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Hi Eric! thanks for the tips! Being able to specify N/C terminus as the ‘mobile’ part is easier to think about! If I understand correctly, I need to pass the correct side of the bond for being smaller to make use of the “move_smaller_side” argument. So, if I’m looking at the C-alpha, then the psi angle would be on the N-terminal side and the phi angle would be on the C-terminal side? So I’ve got this written up (can’t afford to get fancy at the moment) to just assign the angles and move either the N/C terminal side: ``` def straighten_v2(session, mobile_sel, mobile_terminal, noise=5.0): """ Args: mobile_sel (selection): selection of residue regions to be moved, must be a single contiguous region mobile_terminal (str): 'N' or 'C' terminal side noise (float): gaussian standard deviation to 'jitter' angles """ import random mobile_terminal = mobile_terminal.upper() assert mobile_terminal.lower() in ( "c", "n", ), "mobile_terminal can only be N or C" for i, res in enumerate(mobile_sel): # find backbone C-alpha atom = res.find_atom("CA") # handle proline differently (for now) if res.name != "PRO": # bond.smaller_side returns the atom that is on the smaller side for nb, bond in zip(atom.neighbors, atom.bonds): # look at peptide bond atoms only (no beta-carbons) if nb.name == "N": # N-CA -> psi bond (N-terminal) move_smaller_psi = ( bond.smaller_side.name == mobile_terminal ) elif nb.name == "C": # Ca-C -> phi bond (C-terminal) move_smaller_phi = ( bond.smaller_side.name == mobile_terminal ) psi_assgn = random.normalvariate(mu=165.0, sigma=noise) phi_assgn = random.normalvariate(mu=-165.0, sigma=noise) res.set_psi(psi_assgn, move_smaller_side=move_smaller_psi) res.set_phi(phi_assgn, move_smaller_side=move_smaller_phi) ``` It seems to work correctly in some small test cases… but I’ve got a feeling that I did not implement what you meant properly. Is this roughly what you were thinking? Thanks for your help! -D On Dec 18, 2024, at 1:31 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote: On Dec 18, 2024, at 1:26 PM, Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: so if you use "for i, nb in enumerate(atom.neighbors):" to loop through the neighbor atoms Probably even better: for nb, bond in zip(atom.neighbors, atom.bonds): --Eric _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
