[COOT] Problem with Extension- Phosphorylate this Residue
Hello all, this is my first post and I apologize if there is redundancy, but from previous searches of the archives on this board, I did not find an issue similar to mine. I am attempting to phosphorylate a threonine residue, however, I get this error: monomer-molecule-from-3-let-code TPO ) /usr/local/src/Coot/bin/libcheck /usr/local/src/Coot/bin/libcheck ERROR: cant open (lib) list/mon_lib_list exit status: 0 INFO:: libcheck status: 0 libcheck failed to write the output cif file. (get-monomer TPO) The full log is in the attached part. I therefore tried to circumvent this by loading in a clean TPO.cif and TPO.pdb and manually deleting the threonine and renaming / renumbering / merging into the original PDB. When I do a subsequent refinement, I want to edit the sidechain angles, the selection window for choosing which bond angles to modify, there are no applicable selections. I appreciate any feedback the community has to offer and thank you for your time E. Sanchez
[COOT] My mistake, 2nd attempt Extension - Phosphorylate this residue
Hello all, this is my first post and I apologize if there is redundancy, but from previous searches of the archives on this board, I did not find an issue similar to mine. I am attempting to phosphorylate a threonine residue, however, I get this error: monomer-molecule-from-3-let-code TPO ) /usr/local/src/Coot/bin/libcheck /usr/local/src/Coot/bin/libcheck ERROR: cant open (lib) list/mon_lib_list exit status: 0 INFO:: libcheck status: 0 libcheck failed to write the output cif file. (get-monomer TPO) The full log is in the attached part. I therefore tried to circumvent this by loading in a clean TPO.cif and TPO.pdb and manually deleting the threonine and renaming / renumbering / merging into the original PDB. When I do a subsequent refinement, I want to edit the sidechain angles, the selection window for choosing which bond angles to modify, there are no applicable selections. I appreciate any feedback the community has to offer and thank you for your time E. Sanchez
Re: [COOT] To mutate non-standard nucleic acids
Briefly, this is not the way that Coot wants you to do it. Coot wants you to Replace Residue (under modelling). Make sure that your restraints for the modified residue have the group DNA (or RNA), not monomer. Paul. From: Mailing list for users of COOT Crystallographic Software [c...@jiscmail.ac.uk] On Behalf Of Mary Varughese [elizabethvj1...@gmail.com] Sent: 02 June 2010 11:19 To: COOT@JISCMAIL.AC.UK Subject: To mutate non-standard nucleic acids We are working on modified nucleic acids. Using a pdb file of a modified nucleic acid, I want to cut and change the positions of the residues in the nucleic acid chain. I tried it with calculate-- model/fit/refine--rotate/translate zone, although we cut and place it at the correct distance no bond is forming. Is there any way i can do this?
