Thanks, Mitch - this explains it. So it is a remediation issue, because I READ the remediated file remarks in search for an answer, and there is NO more corresponding REMARK 3.
Now, I don't want to be more of a pest than usual, but I am slowly getting worried about this remediation business. What a mess. I have some of my entries that are equally mutilated, lost REMARKS, some of which are really important, and I would strongly suggest that authors check their files. The errors at least in my entries make me look like an amateur. EBI has kindly fixed some manually, but its still a mess. The PDB fellows are aware of the dropped remarks afaik, and I was promised that the remediation (V3.2) of the remediation (V3.1) of the remediation (V3.0) is going to be released in late 2008. Please, get it right this time. Thx, br PS: Half occupied waters in close proximity as a result of correlated split protein-water network conformations are NO ERROR, dear checkers. -----Original Message----- From: Miller, Mitchell D. [mailto:[EMAIL PROTECTED] Sent: Friday, June 20, 2008 2:43 PM To: [EMAIL PROTECTED] Cc: [EMAIL PROTECTED] Subject: RE: [ccp4bb] 2mhb Hi Bernhard, You can always compare it with the version pre-remediation from the "snapshot" archive at the PDB... ftp://snapshots.rcsb.org/ e.g. in 2005 -- ftp://snapshots.rcsb.org/20050106/pub/pdb/data/structures/divided/pdb/mh/pdb 2mhb.ent.Z this shows the coordinates look the same for those 2 columns, so I don't think it is a remediation issue...... >From the original version of remark 3 -- REMARK 3 REFINEMENT. BY THE METHOD OF DEISENHOFER AND STEIGEMANN. 2MHB 23 REMARK 3 ATOMIC RADII WERE REFINED BY THE REAL-SPACE PROCEDURE OF 2MHB 24 REMARK 3 R. DIAMOND. IN THIS REFINEMENT *AMAX* WAS SET TO 2.8 AND 2MHB 25 REMARK 3 *AMIN* EQUALED 1.1. IN *KDAZ* MIN RATIO = 0.01 AND 2MHB 26 REMARK 3 MIN VALUE = 0.01. RADII OF TWO ATOMS ON FORKED SIDE 2MHB 27 REMARK 3 CHAINS (ASP,ASN,ARG,GLU,GLN,THR,VAL,LEU) WERE CONSTRAINED 2MHB 28 REMARK 3 TO BE THE SAME. ONE OCCUPANCY FACTOR PER RESIDUE WAS 2MHB 29 REMARK 3 REFINED. 2MHB 30 So it may be that one column is a refined radii ?? related to ADP in today's parameterization and the other a refined occupancy???? Not really sure, one would have to look back at the papers describing the refinement method to have a better idea. (Although one issue I would raise with the PDB about the remediated file is that they should have dumped the existing Remark 3 refinement details comment into the free text field - " REMARK 3 OTHER REFINEMENT REMARKS:" == mmCIF _refine.details token. It is in the mmCIF formatted file under the loop over _database_PDB_remark.id / _database_PDB_remark.text but those details are lost in the PDB formatted remediated file.) Regards, Mitch -----Original Message----- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Bernhard Rupp Sent: Friday, June 20, 2008 2:06 PM To: [email protected] Subject: [ccp4bb] 2mhb Dear All - can someone please explain to me the last 2 dat items in the 2mhb ATOM recs? Looks like X Y Z followed by B and ?? Is this some historic legacy (1977) or another remediation incident? Obviousy this is not the standard format it purports to be in, but there might be good reasons. No access to orig citation... Thx, br ----------------------------------------------------------------- Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 [EMAIL PROTECTED] [EMAIL PROTECTED] http://www.ruppweb.org/ ----------------------------------------------------------------- The hard part about playing chicken is to know when to flinch -----------------------------------------------------------------
