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> All the atoms are at right place. But some bonds of CYSP are missing in > the pdb file, such as the bonds from the methyl to MTSL ring, the bonds > from CL1 to MTSL ring. It looks like the MTSL ring, each methyl group > and sulphur atoms are treated as individual moiety without bond > connection. This observation happens in both of the demo new.pdb and my > own pdb output. I am not concern whether these missing bonds will affect > future refinement. BTW, I display the pdb using sibyl. > I think the lack of bonds is just what sibyl deduced, and they really are present in the psf. It's not too hard to check this - look for the appropriate atom indices in the psf's bond list. Alternatively, you might try a visualization program such as VMD, which can read both psf and pdb info. regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD8DBQFD4PbgPK2zrJwS/lYRAtoOAJ9eFzm/+cnqDL/nX6EN06GaL0CVwQCfdtu5 fVoSd96Ja84EHMvbDrwvct0= =cph5 -----END PGP SIGNATURE-----
