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Hello Andreas-- > > I found solutions for both problems. First I found out that Xplor-NIH > didn't get the NOEs calculated by ARIA/CNS right. The problem is that > ambiguous or even unambiguous restraints, that are separated by an "or" > statement aren't recognized. Xplor-NIH kept reading only the first line > of such a statement and ignored the rest without a single sign of a > warning or something like that. If the input is e. g.: > > assign (segid " " and resid 103 and name HA) (segid " " and > resid 32 and name HD22) 2.666 0.853 0.853 ! spec=13C NOESY, no=0, > id=1648 > > or (segid " " and resid 103 and name HA) (segid " " and > resid 32 and name HD21) > > or (segid " " and resid 103 and name HA) (segid " " and > resid 32 and name HD23) > > Xplor-NIH only read the first line (ignoring the two lines beginning > with "or") and went on to the next NOE without ANY sign of this behavior > except from a resulting structure that was quite different from the one > using ARIA/CNS. As you discovered, this is not a valid assignment NOE statement for the Python NOEPot term, or for the XPLOR NOE term. The syntax for the assignment statement for these terms are described, respectively, in http://nmr.cit.nih.gov/xplor-nih/doc/current/python/ref/noePot.html http://nmr.cit.nih.gov/xplor-nih/doc/current/xplor/node362.html It would be nice if ARIA could have a conversion utility to format used by Xplor-NIH. Alternatively you (or someone else) could request that the extended syntax be supported by Xplor-NIH. > > The deviation from planarity could be stopped by simply adding > potList.add(XplorPot("DIHE")) > to the other other invocations This is not a good idea. While the ligand might remain planar, you will likely bias protein dihedral angles. The standard in Xplor-NIH is for planarity-maintaining terms to be included in the IMPR term. Your best bet is to change the relevant terms into impropers. The IVM can also be used to fix rigid regions. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.1 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFGQeQfPK2zrJwS/lYRAkJWAJ48L+kcgsiw54DUEaM/Uf04GUTt/gCfVBpI gNbTMGBjihT7Z2ggjXHRHns= =2CEm -----END PGP SIGNATURE-----
