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(13) CIF and PDB: report from Paula
- To: COMCIFS@uk.ac.iucr
- Subject: (13) CIF and PDB: report from Paula
- From: bm@uk.ac.iucr (Brian McMahon)
- Date: Thu, 18 Nov 93 11:43:38 GMT
Dear Colleagues The PDB at Brookhaven National Labs was site visited in June of this year. Results of the site visit are not yet official, but it is widely understood that the review was unfavorable. There will be a call for proposals for an open competition for this facility. This call has not yet gone out, but it is expected shortly. Funding will be through a multi-agency mechanism, with funds coming from the National Science Foundation, the National Institutes of Health and the Department of Energy. NSF will administer the grant evaluation and awarding process. The current PDB operation at Brookhaven will be funded on continuing funds during the transition. They of course will be able to, and are fully expected to, respond to the call for proposals. In anticipation of a completely revised application (I assume), major changes have begun to happen. Last week Tom Koetzle resigned as Director, and Dave Stampf has been appointed Interim Acting Director, or some such title. We are told that interviews are being conducted for a new Director, but I know no details about that. One of the technical problems that we have had in finalizing CIF as a new format for the Protein Data Bank has been less than effective communications with the staff at the PDB. The evidence of a meeting that was held last Friday is that this is no longer a problem. The meeting was attended by Phil Bourne, Helen Berman and myself representing mmCIF and Dave Stampf, Dejun Xue and Nancy Oeder representing the PDB. The goal was to see if we can identify the holes in the current mapping of PDB to CIF and vice versa using some of the current tools, Phil's pdb2cif awk script and Dejun's tool for going in the other direction. It was a very productive meeting - particularly from my standpoint, as it revealed that most of the obvious problem are with the tools and not with the dictionary. But one thing that came out of our discussion is very relevant to COMCIFS, and that is what we are currently calling the External Reference Files. The particular issue is the keywords that we want to use at several levels for describing the asymmetric unit structure and the biological structure. Everyone agrees that keywords are useless unless a consistent set is employed. But we disagree about how to do this when mmCIF hits the streets. The two viewpoints are the following: Paula) The set of keywords will grow as science grows, and so we want to manage them in a way that will be flexible and easily expanded. Therefore it would be a strategic error to embed them in the mmCIF dictionary as enumeration values for data items such as (for example) _struct_biol_keyword. Ultimately, the keywords will be managed through external reference files, but since that formalism does not yet exist, we should enter them in the current dictionary as examples, much as we have done with the least-squares restraints. Everyone Else) The list of keywords will indeed grow, but not so fast that we cannot manage the list within the constraints of COMCIFS management of the dictionary. We would like to use ERFs for keywords, but we don't have ERFs yet, and we have to do something now. Therefore, keywords must be defined in enumeration lists. It really was all against one on this issue, and I see only two ways out of this. 1) Solve the ERF problem *NOW* 2) Give in and put the keywords in the enumeration list. As an exercise, Dave Stampf looked at the current PDB files, and found about 250 different HEADER records (the only attempt at keywording current PDB files). There is strong evidence here of the problems of non-enumerated keywords, and my guess is that the list will reduce to about 100 after it is cleaned up. I will forward a copy to you. A subtext issue in all of this is the issue of updating enumeration lists. To my thinking, doing this violates the assumptions of immutability of officially sanctioned CIF data definitions, but we have already agreed to do this with the core (for example, in adding y as a synonym for yes). This is an issue that COMCIFS should address right away. List of PDB Header records ACID ANHYDRIDE HYDROLASE ACYL-COENZYME A BINDING PROTEIN AIDS-RELATED VIRUS GAG POLYPROTEIN ALPHA-AMYLASE INHIBITOR AMINO-ACID TRANSPORT AMINOTRANSFERASE ANTI-HYPERTENSIVE, ANTI-VIRAL PROTEIN ANTIBACTERIAL PROTEIN ANTIFREEZE PROTEINS APOPROTEIN BACTERIAL ENCAPSULATION BILIN BINDING BINDING PROTEIN BINDING PROTEINS BIOTIN BINDING PROTEIN CALCIUM BINDING CALCIUM BINDING PROTEIN CALCIUM-BINDING PROTEIN CALCIUM/PHOSPHOLIPID BINDING CARBON-OXYGEN LYASE CARBOXYLIC ESTER HYDROLASE CARBOXYLIC ESTER HYDROLASE ZYMOGEN CARDIO PICORNAVIRUS COAT PROTEIN CHAPERONE PROTEIN CHEMOTAXIS CHROMOSOMAL PROTEIN COAGULATION INHIBITOR COAT PROTEIN (VIRAL) COMPLEMENT FACTOR COMPLEX (ANTIBODY-ANTIGEN) COMPLEX (DEOXYRIBONUCLEIC ACID/SPERMINE) COMPLEX (LIGASE-T/RNA$) COMPLEX (PROTEINASE-INHIBITOR) COMPLEX (PROTEINASE/INHIBITOR) COMPLEX(ANTIBODY-ANTIGEN) COMPLEX(SERINE PROTEINASE-INHIBITOR) CONTRACTILE SYSTEM PROTEIN CONTRACTILE SYSTEM PROTEINS CYTOKINE CYTOLYTIC PROTEIN CYTOTOXIN DEFENSIN DEHALOGENASE DEOXYRIBONUCLEIC ACID DNA BINDING DNA BINDING (VIRAL) DNA BINDING REGULATORY PROTEIN DNA-BINDING MOTIF DNA/RNA ELECTRON TRANSFER (FLAVOPROTEIN) ELECTRON TRANSFER (IRON-SULFUR PROTEIN) ELECTRON TRANSFER(CUPROPROTEIN) ELECTRON TRANSFER(IRON-SULFUR PROTEIN) ELECTRON TRANSFER(IRON-SULFUR) ELECTRON TRANSPORT ELECTRON TRANSPORT (COPPER BINDING) ELECTRON TRANSPORT (CYTOCHROME) ELECTRON TRANSPORT (HEME PROTEIN) ELECTRON TRANSPORT PROTEIN ELECTRON TRANSPORT PROTEIN (CYTOCHROME) ELECTRON TRANSPORT PROTEIN(CUPROPROTEIN) ELECTRON TRANSPORT(CYTOCHROME) ELONGATION FACTOR ENDODEOXYRIBONUCLEASE ENDONUCLEASE EXCITATION ENERGY TRANSFER EYE LENS PROTEIN FATTY ACID SYNTHESIS PROTEIN FATTY ACID-BINDING PROTEIN FELIX GENE REGULATING PROTEIN GENE REGULATORY PROTEIN GLYCOGEN PHOSPHORYLASE GLYCOPROTEIN GLYCOSIDASE GLYCOSIDASE INHIBITOR GROWTH FACTOR HEME PROTEIN OF ELECTRON TRANSPORT HEPATIC LECTIN HISTOCOMPATIBILITY ANTIGEN HORMONE HORMONE (MUSCLE RELAXANT) HYDRO-LYASE HYDROLASE HYDROLASE (SERINE PROTEINASE) HYDROLASE (ACID PROTEASE) HYDROLASE (ACID PROTEINASE) HYDROLASE (ASPARTIC PROTEINASE) HYDROLASE (C-TERMINAL PEPTIDASE) HYDROLASE (CARBOXYLIC ESTER) HYDROLASE (ENDORIBONUCLEASE) HYDROLASE (METALLOPROTEINASE) HYDROLASE (NUCLEIC ACID, RNA) HYDROLASE (NUCLEIC ACID,RNA) HYDROLASE (O-GLYCOSYL) HYDROLASE (PEPTIDE) HYDROLASE (PHOSPHORIC DIESTER) HYDROLASE (PHOSPHORIC DIESTER, RNA) HYDROLASE (PHOSPHORIC MONOESTER) HYDROLASE (PROTEINASE) HYDROLASE (SERINE PROTEINASE) HYDROLASE (SULFHYDRYL PROTEINASE) HYDROLASE ZYMOGEN HYDROLASE ZYMOGEN (SERINE PROTEINASE) HYDROLASE(ACID PROTEINASE ZYMOGEN) HYDROLASE(ACID PROTEINASE) HYDROLASE(ACTING IN CYCLIC AMIDES) HYDROLASE(ACTING IN CYCLICAMIDINES) HYDROLASE(ACTING ON ACID ANHYDRIDES) HYDROLASE(ALPHA-AMINOACYLPEPTIDE) HYDROLASE(ASPARTIC PROTEINASE) HYDROLASE(ASPARTYL PROTEINASE) HYDROLASE(CARBOXYL ESTER) HYDROLASE(CARBOXYLIC ESTER) HYDROLASE(CARBOXYLIC ESTERASE) HYDROLASE(ENDORIBONUCLEASE) HYDROLASE(O-GLYCOSYL) HYDROLASE(SERINE PROTEINASE) HYDROLASE(ZYMOGEN) HYDROLASE-TRANSPEPTIDASE HYDROPHOBIC SEED PROTEIN IMMUNOGLOBULIN IMMUNOGLOBULIN BINDING PROTEIN IMMUNOGLOBULIN(PART)SEQUESTERS ANTIGENS IMUNOGLOBULIN INFLUENZA VIRUS HEMAGGLUTININ INSULIN AND INSULIN-LIKE HORMONES INTEGRAL MEMBRANE PROTEIN PORIN INTRAMOLECULAR OXIDOREDUCTASE IRON STORAGE IRON TRANSPORT PROTEIN ISOMERASE ISOMERASE(INTRAMOLECULAR ALDOSE/KETOSE) ISOMERASE(INTRAMOLECULAR LYASE) ISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE) ISOMERASE(INTRAMOLECULAR OXIDOREDUCTSE) LECTIN LECTIN (AGGLUTININ) LEUCINE ZIPPER LIGASE (SYNTHETASE) LIGASE(AMIDE SYNTHETASE) LIGHT HARVESTING PROTEIN LIPOCALIN LIPOPROTEIN LYASE (ALDEHYDE) LYASE(ACTING ON POLYSACCHARIDES) LYASE(CARBON-CARBON) LYASE(CARBON-OXYGEN) LYASE(OXO-ACID) LYMPHOKINE METALLOTHIONEIN NEUROTOXIN NEUROTOXIN (POST-SYNAPTIC) NUCLEIC ACIDS (DNA/RNA) NUCLEOTIDYLTRANSFERASE ONCOGENE PROTEIN OXIDO-REDUCTASE OXIDO-REDUCTSE(ALDEHYDE/DONR,NAD/ACCPT) OXIDOREDUCTASE OXIDOREDUCTASE (/NAD$(A)-ALDEHYDE(D)) OXIDOREDUCTASE (CH-NH(D)-NAD OR NADP(A)) OXIDOREDUCTASE (CH-OH(D)-CYTOCHROME(A)) OXIDOREDUCTASE (FLAVOENZYME) OXIDOREDUCTASE (H2O2 (A)) OXIDOREDUCTASE (H2O2 ACCEPTOR) OXIDOREDUCTASE (H2O2(A)) OXIDOREDUCTASE (INCORPORATION OF O2) OXIDOREDUCTASE (NAD(A)-CHOH(D)) OXIDOREDUCTASE (OXYGEN(A)) OXIDOREDUCTASE (QUINOPROTEIN) OXIDOREDUCTASE (SUPEROXIDE ACCEPTOR) OXIDOREDUCTASE(ACTING ON NADH OR NADPH) OXIDOREDUCTASE(ALDEHYDE(D)-NAD(A)) OXIDOREDUCTASE(CHNH(D)-NAD+ OR NADP+(A)) OXIDOREDUCTASE(CHOH(D)-NAD(A)) OXIDOREDUCTASE(H2O2(A)) OXIDOREDUCTASE(NAD(A)-CHOH(D)) OXIDOREDUCTASE(NADP+(A),FERREDOXIN(A)) OXIDOREDUCTASE(NITRIC OXIDE(A)) OXIDOREDUCTASE(OXYGENASE) OXIDOREDUCTASE, CHOH DONOR, NAD ACCEPTR OXIDOREDUCTASE/ELECTRON TRANSPORT OXO-ACID-LYASE OXYGEN BINDING OXYGEN STORAGE OXYGEN TRANSPORT OXYGEN TRANSPORT PROTEIN PANCREATIC HORMONE PARVOVIRUS COAT PROTEIN PENTOSYLTRANSFERASE PEPTIDE ANTIBIOTIC PERIPLASMIC BINDING PROTEIN PHOSPHORIC DIESTER HYDROLASE PHOSPHOTRANSFERASE PHOSPHOTRANSFERASE (CARBOXYL ACCEPTOR) PHOSPHOTRANSFERASE(CARBOXYL AS ACCEPTOR) PHOTORECEPTOR PHOTOSYNTHETIC REACTION CENTER PICORNAVIRUS PLANT SEED PROTEIN PLANT SEED STORAGE PROTEIN (VICILIN) PLASMINOGEN ACTIVATOR POSTSYNAPTIC NEUROTOXIN PRELIMINARY PRESYNAPTIC NEUROTOXIN PROTEIN INHIBITOR PROTEINASE INHIBITOR PROTEINASE INHIBITOR (CHYMOTRYPSIN) PROTEINASE INHIBITOR (KAZAL) PROTEINASE INHIBITOR (SUBTILISIN BPN*) PROTEINASE INHIBITOR (TRYPSIN) REDUCTASE RETINOL TRANSPORT RHINOVIRUS COAT PROTEIN RIBONUCLEIC ACID RIBOSOMAL PROTEIN SEA ANEMONE TOXIN SERINE PROTEINASE SERINE PROTEINASE INHIBITOR SERPIN SIGNAL TRANSDUCTION PROTEIN SITE-SPECIFIC RECOMBINASE STEROID BINDING STRUCTURAL (CELL ENVELOPE COMPONENT) SWEET TASTING PROTEIN SYNTHETIC PROTEIN MODEL T-CELL SURFACE GLYCOPROTEIN TEXTURE OF CONNECTIVE TISSUE THYMIDINE PHOSPHORYLASE TOXIN TOXIN (HEMOLYTIC POLYPEPTIDE) TRANSCRIPTION REGULATION TRANSFERASE TRANSFERASE (ACYLTRANSFERASE) TRANSFERASE (CARBAMOYL-P,ASPARTATE) TRANSFERASE (METHYLTRANFERASE) TRANSFERASE (METHYLTRANSFERASE) TRANSFERASE (PHOSPHORYL) TRANSFERASE (PHOSPHOTRANSFERASE) TRANSFERASE(AMINOTRANSFERASE) TRANSFERASE(PHOSPHO,ALCOHOL ACCEPTOR) TRANSFERASE(PHOSPHORYL,ALCOHOL ACCEPTR) TRANSFERASE(PHOSPHOTRANSFERASE) TRANSFERASE(THIOSULFATE,CYANIDE SULFUR) TRANSPORT (THYROXINE,RETINOL) IN SERUM TRANSPORT AND PROTECTION PROTEIN TYPE 1 COPPER PROTEIN VIRUS ZINC FINGER /DNA$ BINDING DOMAIN ZINC FINGER DNA BINDING DOMAIN - Paula
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