Hi Charles, My initial structure was generated from Cyana 2.0. I thought the error could arise from atom numbering mismatching, so spent a bit time managing to match the numbering of atoms in pdb and psf so that they are identical but the error is the same. So it could be the problem of my initial structure. But how do you define a decent structure? Any measures? I thought mine was good enough since it was folded, converged in structure calculation ...
BTW, do I have to add ANI pseudo-atoms to run refine.py against RDC data? If yes, how? Thanks, Yufeng --- [email protected] wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > Hello Yufeng-- > > > > > New to xplor, I trying to incorporate RDC data in > > structure refinement following examples in > > eginput/gb1_rdc. > > > > I modified the refine.py to load my data. But I > got a > > message about topology error. The related error > > message is attached at the end of this email. The > > following is the difference between the modified > and > > the original refine.py from gb1_rdc: > > > > > > ====== Error Message > ============================== > > > > > > calcD_G: singular D matrix: { { 0 } } > > H matrix: { { 0, 0, 0, 0, 0, 0 } } > > node level: 367 > > number of children: 0 > > atoms: > > 1906 GLN 122 CD : { 10000, 10000, 10000 } > > 1909 GLN 122 HE21 : { 10000, 10000, 10000 > } > > 1910 GLN 122 HE22 : { 10000, 10000, 10000 > } > > 1907 GLN 122 OE1 : { 10000, 10000, 10000 } > > 1908 GLN 122 NE2 : { 10000, 10000, 10000 } > > > > it looks like you don't have decent starting > coordinates- if this is the > case, you should probably use anneal.py instead. If > you do have a decent > starting model, something else must be wrong. > > regards-- > Charles > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.2.1 (GNU/Linux) > Comment: Processed by Mailcrypt 3.5.8 > <http://mailcrypt.sourceforge.net/> > > iD8DBQFDb3IlPK2zrJwS/lYRAufMAJ4z3VDDi/zpZQ1l1I6zTI1TMQGq0wCfaHdf > ZwEHrhrkYnBG6FweNzp96WA= > =caBf > -----END PGP SIGNATURE----- > __________________________________ Yahoo! Mail - PC Magazine Editors' Choice 2005 http://mail.yahoo.com
