[ccp4bb] FW: [ccp4bb] 2mhb

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: 2mhb
From: "Santarsiero, Bernard D {- dot -} " bds {- at -} UIC {- dot -} EDU
Date: 2008-06-20

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From: Alexandra Deaconescu deacona {- at -} BRANDEIS {- dot -} EDU
Date: 2008-06-21

Subject: FW: 2mhb
From: Bernhard Rupp bernhardrupp {- at -} SBCGLOBAL {- dot -} NET
Date: 2008-06-21

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:mmiller@slac.stanford.edu]
Sent: Friday, June 20, 2008 2:43 PM
To: bernhardrupp@sbcglobal.net
Cc: info@rcsb.org
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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Bernhard Rupp
Sent: Friday, June 20, 2008 2:06 PM
To: CCP4BB@JISCMAIL.AC.UK
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
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CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: 2mhb
From: "Santarsiero, Bernard D {- dot -} " bds {- at -} UIC {- dot -} EDU
Date: 2008-06-20

Next message:
Subject: crystallization incubators
From: Alexandra Deaconescu deacona {- at -} BRANDEIS {- dot -} EDU
Date: 2008-06-21