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.
Thanks BAINAN WU Structural Biology St. Jude Children's Research Hospital 901.495.3176(2240) [email protected] -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of [email protected] Sent: Wednesday, February 01, 2006 6:52 AM To: Wu, Bainan Cc: [email protected] Subject: Re: [Xplor-nih] how to incorporate into MTSL into a protein? . . . . -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi-- > > "PARRDR-ERROR: duplication of nonbonded entry CS2", or, > "PARRDR-ERROR: duplication of bond entry C3S8 HA", or, > "PARRDR-ERROR: duplication of angle C3S6 CSN2 C3S7" > It looks like a parameter file somehow got loaded twice. > I check the output pdb file and find that the rotatable bonds between > cysteine and the ring of MTSL are missing in the final structure. Is > this related to the above error reports? Maybe not, because it seems > these bonds are missing as well in the demo output. > Can you tell us which atoms are missing (by atom name)? I don't see missing atoms in the output of the shipped version of addAtoms.py. regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD8DBQFD4K79PK2zrJwS/lYRAh2EAJwJdUaP3lHQTx5f56A5Uoma8680mgCcC9Cs 2AoYrR2502OBZmSzkPC8jP4= =VmDk -----END PGP SIGNATURE-----
