1CRN for example has disulphide bonds which are covalant and thats why set_dihedral does not work. I think its the bug, which tells you that it has been setted to zero. So you have to remove the disulphide bonds before setting the dihedral angles.
you can do so by unbond r. cys and n. sg, r. cys and n. sg and then PyMOL>set_dihedral 21/n, 21/ca, 21/c, 22/n, 0.0 SetDihedral: adjusted to 0.000 PyMOL>get_dihedral 21/n, 21/ca, 21/c, 22/n cmd.get_dihedral: -0.000 degrees. cheers, Abhinav. On 11/13/06, Chris Weichenberger <cwe...@cosy.sbg.ac.at> wrote:
Dear PyMol users, I am trying to set dihedral angles in a protein. Unfortunately, the set_dihedral command is not documented, but it looks like it is the same as the get_dihedral with an additional value for the angle to set. I tried to set the dihedral angle for the protein crambin (PDB code 1CRN). First I query the angle: PyMOL>get_dihedral 21/n, 21/ca, 21/c, 22/n cmd.get_dihedral: 136.344 degrees. I then assume that this command sets the dihedral angle to 0: PyMOL>set_dihedral 21/n, 21/ca, 21/c, 22/n, 0.0 SetDihedral: adjusted to 0.000 Therefore, it should be the case that the angle is 0, however, it is still the old value: PyMOL>get_dihedral 21/n, 21/ca, 21/c, 22/n cmd.get_dihedral: 136.344 degrees. The graphics has changed but the molecule's overall topology still looks like the original one. Also, repeating the above set_dihedral command results in successively altered graphics, which contradicts my inuition that setting a dihedral angle to the same fixed value should not result in any changes at all. Has anyone played around with this command and can report its proper usage? My ultimate goal is to write an animation that folds a protein from a more or less linear chain to its final correct 3D structure by interpolating dihedral angles. I am running PyMol version 0.97. Thanks for any help on this topic. _X ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
