> I think its the bug, > which tells you that it has been setted to zero.
Yes, this is a flaw. Constrained by the laws of topology, PyMOL cannot rotate a dihedral that is contained within a cyclic structure. However, instead of complaining about the situation as it probably should, it instead rotates the entire cyclic structure about the central bond of the dihedral. Cheers, DeLano Scientific LLC Email Support Services > -----Original Message----- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of Abhinav Verma > Sent: Tuesday, November 14, 2006 6:07 AM > To: Chris Weichenberger; pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] set_dihedral command > > 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 > <mailto: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 > <https://lists.sourceforge.net/lists/listinfo/pymol-users> > > > >
