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On further investigation there would appear to be (at least) two different water-numbering conventions operating: the difference between them can be seen by looking at the 'REMARK 525' records, which are presumably generated at the deposition sites. The first is exemplified by entry 2A1M: REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH 137 DISTANCE = 10.36 ANGSTROMS REMARK 525 HOH 172 DISTANCE = 6.77 ANGSTROMS REMARK 525 HOH 173 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH 184 DISTANCE = 13.94 ANGSTROMS REMARK 525 HOH 193 DISTANCE = 8.51 ANGSTROMS REMARK 525 HOH 205 DISTANCE = 9.91 ANGSTROMS REMARK 525 HOH 240 DISTANCE = 5.41 ANGSTROMS REMARK 525 HOH 250 DISTANCE = 7.49 ANGSTROMS REMARK 525 HOH 252 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH 262 DISTANCE = 10.28 ANGSTROMS REMARK 525 HOH 276 DISTANCE = 5.67 ANGSTROMS REMARK 525 HOH 281 DISTANCE = 5.51 ANGSTROMS REMARK 525 HOH 287 DISTANCE = 11.73 ANGSTROMS and the second by entry 2J0S: REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES ARE GIVEN CHAIN IDENTIFIERS TO REMARK 525 INDICATE THE PROTEIN CHAIN TO WHICH THEY ARE MOST CLOSELY REMARK 525 ASSOCIATED WITH: REMARK 525 PROTEIN CHAIN SOLVENT CHAIN REMARK 525 A Z REMARK 525 C X REMARK 525 D W REMARK 525 E V REMARK 525 T G In the first example water atoms _are_not_ assigned a chain ID so all 'residue numbers' have to be unique and may need to be changed, as explained in the RCSB document. In the second example water atoms _are_ assigned a chain ID, I guess using Watertidy either by the depositor or by the deposition site. So the numbers need not be unique and the original numbers could be retained (whether they are or not I've no idea). If it is really the case that different numbering conventions are being enforced at the various deposition sites (presumably RCSB & EBI resp. in the two cases above), then clearly depending on which convention you want to adhere to, choose the deposition site appropriately! -- Ian > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On > Behalf Of Ian Tickle > Sent: 06 December 2006 16:32 > To: Sue Roberts; Gerard DVD Kleywegt > Cc: CCP4 Bulletin Board > Subject: RE: [ccp4bb]: refmac PDB header > > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > > This has a description: > > http://deposit.rcsb.org/depoinfo/download/dp.pdf > > It says that renumbering is only done 'when necessary' or 'if > it (the present numbering) will cause problems later'. An > example is given: > > If the waters have only one chain ID, this chain ID can be > removed through struct_biol_gen in ADIT . If waters in a > particular entry have more than one chain ID and have similar > numbering (for example, water chain A 1-100 and water chain B > 1-100), the chain ID must be removed and the waters must be > renumbered. > > -- Ian > > > -----Original Message----- > > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On > > Behalf Of Sue Roberts > > Sent: 06 December 2006 16:00 > > To: Gerard DVD Kleywegt > > Cc: CCP4 Bulletin Board > > Subject: Re: [ccp4bb]: refmac PDB header > > > > *** For details on how to be removed from this list visit the *** > > *** CCP4 home page http://www.ccp4.ac.uk *** > > > > > > Hello, > > > > Gerard, 'DVD", wrote the reply below. > > > > > > > >> Would it be possible to make a lobby and get the PDB NOT > > TO CHANGE > > >> anything we don´t want to have changed in the structures > that are > > >> supposed to be > > > > > > alternatively - we could all follow the convention from the start > > > > So, how can we find out what this convention is? I just > browsed the > > depositor information at rcsb and didn't find any information on > > solvent or ligand numbering. (Granted, I didn't do an exhaustive > > search). > > > > Sue > > > > > > > > > > Disclaimer > > This communication is confidential and may contain privileged > information intended solely for the named addressee(s). It > may not be used or disclosed except for the purpose for which > it has been sent. If you are not the intended recipient you > must not review, use, disclose, copy, distribute or take any > action in reliance upon it. If you have received this > communication in error, please notify Astex Therapeutics Ltd > by emailing [EMAIL PROTECTED] and destroy all > copies of the message and any attached documents. > > > > Astex Therapeutics Ltd monitors, controls and protects all > its messaging traffic in compliance with its corporate email > policy. 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