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	PDB REFERENCE MANUAL
		The primary function of PDB is to allow the user to schedule planning problems to be run by the planner, record the actions taken by the planner, and then reconstruct that information in a meaningful way.
		PDB is an interactive application which makes the UCPOP planning process more accessible to the user by the use of graphical interfaces to the planning process.
		PDB prints plans in the following manner: the initial state is printed first, then the steps in order to the goal state.
	www.cs.washington.edu /ai/pdb/pdb.html (2780 words)

	Protein Database (PDB) and Molecular Database (MOL) Geometry Import Converter
		Due to the large number of spheres and cylinders that often are used to represent the contents of a PDB file the imported file may be slow to render or to display interactively.
		As described on the PDB database WEB page: http://www.rcsb.org/pdb/experimental_methods.html, most of the three-dimensional macromolecular structure data in the Protein Data Bank were obtained by one of three methods: X-ray crystallography (over 80%), solution nuclear magnetic resonance (NMR) (about 16%) or theoretical modeling (2%).
		The PDB file format is a text-based file format that is designed to convey information about the structure of molecules; namely organic compounds such as proteins.
	www.okino.com /conv/imp_pdb.htm (3103 words)

	D.W. Fearn - PDB Passive Direct Box Instructions (Site not responding. Last check: 2007-10-23)
		The PDB takes a low-level, high-impedance, unbalanced signal (such as from an electric bass guitar) and converts the signal to a mic-level, low-impedance, balanced signal to be fed to a professional microphone preamplifier.
		To use the PDB, plug the instrument into the 1/4” jack labeled “INST.” The output of the PDB is available on the male XLR connector labeled “MIC LEVEL OUT.” Use a high-quality balanced mic cable with the appropriate connectors to connect the PDB to your microphone preamplifer.
		The PDB is designed to accommodate signals as high as 2 volts peak-to-peak and it is highly unlikely to be overloaded by any typical instrument.
	www.dwfearn.com /pdbman.html (453 words)

	August 6 PDB
		Although the PDB referred to the possibility of hijackings, it did not discuss the possible use of planes as weapons.
		When this PDB item was presented to the President on August 6, 2001, his PDB briefer told him that it was prepared in response to the President's previous questions.
		The copy of the PDB that has been released is a copy of the PDB prepared for the President, except that three redactions have been made to protect the names of foreign governments that provided information to CIA.
	www.agonist.org /annex/pdb.htm (1262 words)

	PDB Converter (Site not responding. Last check: 2007-10-23)
		PDB Converter is a Windows 95/98/98SE/Me/NT/2000/XP application that can create “NSBasic for Palm™”-compatible PDB files interactively (by direct data entry into its spreadsheet) or by converting existing text files (including tab-delimited files), quoted and non-quoted comma separated values (CSV) files, and Excel 4.0 and 5.0 worksheets.
		PDB Converter accepts command-line filenames, and determines the data type and direction based on the number of arguments, and the extensions.
		PDB Converter can create PDB’s as single records with many fields (one for each row:column item in the database), or a single record and a single field, concatenating all text from all rows and columns into a single, long string, with or without line feeds after each record in the original database.
	www.mverive.com /pdbconverter.htm (2326 words)

	- About Pdb
		JÃ¶nkÃ¶ping-based Pdb was founded in 1983, so itâs been around for a long time...
		Pdb is a staff-owned company, which currently has just over 60 employees.
		Pdb has during the last yearsÂ become classified with highest credit ratingÂ by DandB.
	www.pdb.se /?id=211 (270 words)

	ASPN : Python Cookbook : sane tab completion in pdb (Site not responding. Last check: 2007-10-23)
		If on startup pdb finds a.pdbrc file in either a user's home directory or in the current directory it runs each line as though it were typed into the prompt.
		However, running pdb via "python -m" uses execfile to start your script, and that is executed in a new code block.
		The side effect of this is that from.pdbrc.py the Pdb class object is not the one that is being used to run this pdb session.
	aspn.activestate.com /ASPN/Cookbook/Python/Recipe/498182 (574 words)

	ASPN : Palm::PDB 1.8 (Site not responding. Last check: 2007-10-23)
		By itself, the PDB module is not terribly useful; it is intended to be used in conjunction with supplemental modules for specific types of databases, such as Palm::Raw or Palm::Memo.
		Looks through the list of records in $pdb, and returns a reference to the record with ID $id, or the undefined value if no such record was found.
		It takes $pdb's sort block, $pdb->{sort}, and returns a string of raw data that can be written to the database file.
	aspn.activestate.com /ASPN/CodeDoc/p5-Palm/Palm/PDB.html (1370 words)

	pdb: A simple C++ PDB reader
		This is a simple C++ PDB reader along with a couple of programs which use it to manipulate pdb files (applying a rigid transform or splitting/merging).
		To split a pdb file into one new file per model in the old file, run "pdb_split old.pdb new%d.pdb" where the argument newd.pdb is used to generate file names using printf conversions.
		To use it, call the program with the pdb you with to transform and the pdb file to write as arguments and paste the 3 lines of the Dali file containing the transform into standard input.
	graphics.stanford.edu /~drussel/pdb (709 words)

	MMTSB - All-atom Modeling: PDB File Manipulation
		PDB format files from the Protein Data Bank or other sources usually require minor modifications with respect to residue and atom names before they can be read into CHARMM or Amber, the main modeling packages used by the MMTSB Tool Set.
		Other PDB file manipulations that may also need to be done but cannot be done automatically involve changing residue numbering and assigning chain IDs.
		When PDB files are read into CHARMM they are expected to have a four letter segment ID starting at position 73 at the end of each PDB ATOM line.
	mmtsb.scripps.edu /software/tutorial/allatom-pdbfiles.html (1182 words)

	PDB and HDF5 Compared (Site not responding. Last check: 2007-10-23)
		PDB appears to scale more smoothly to larger I/O sizes in these first two graphs, taking less time than HDF5, though the percent difference is fairly small and may be due to noise introduced by other jobs on the system.
		We also see that PDB and HDF5 restart performance is comparable in Graph IX where both libraries target their files though a little extra cost is taken during the creation of the PDB file to obtain similar restart times.
		It appears that PDB is somewhat less efficient here and this cost must be taken at either the time of creation of the file (Graph IX) or when the file is read (Graph X), if it is the case that the file is transfered between machines of a different architecture.
	pact.llnl.gov /benchmarks.html (3872 words)

	PDB Plugin, Version 1.14
		Since PDB files can only store 99,999 atoms without overrunning the columns designated for atom indices etc, the PDB plugin doesn't directly use the atom indices specified in the PDB file as its own indices, instead it keeps its own independent atom index counter, allowing it to read files containing millions of atoms.
		Various PDB record types and fields are ignored by VMD, in general VMD doesn't do anything with the sequence data or crystallography-specific fields in the format presently.
		All unused PDB records are returned as remark data by the PDB plugin, allowing this information to be parsed and accessed by plugins.
	www.ks.uiuc.edu /Research/vmd/plugins/molfile/pdbplugin.html (540 words)

	PDB FILE FORMAT FAQ
		The PDB Chemical Component Dictionary (formerly the HET Group Dictionary) is available in PDB [8.5 Mb] and mmCIF [15.7 Mb] formats, and is updated weekly.
		This page provides descriptions and examples of the contents of the PDB format and mmCIF format Chemical Component Dictionaries as well as a description of the contents of a Ligand Depot entry.
		Both the PDB format [8.5 Mb] and mmCIF format [15.7 Mb] Chemical Component Dictionaries describe all residues in the PDB, both standard and non-standard, in addition to all the small molecule ligands.
	deposit.pdb.org /cc_dict_tut.html (1167 words)

	PDB Class Reference
		The PDB class has several enhancements to the Brookhaven Protein DataBank specification: four character residue names, the PDBRUN set of scene annotation records (see reference in the See Also section), and atom serial number overflow protection.
		Change the PDB record type of the instance and reinitialize all the fields to default values (zero in all cases except for an ATOM's occupancy which defaults to 1.0).
		To be entirely consistent with the PDB format, the programmer should put those blanks in before using the c_str member function.
	www.cgl.ucsf.edu /Research/otf/lib/pdb (971 words)

	The RSDS pdb format
		Since the PDB format keeps changing, you can't expect visual tools to keep up with the changes and the files are best viewed using a hex editor such as Paws, or dumped to a file or printed using a hex filedump program such as Borland's tdump.
		In pdb files, it might be more appropriate to call the blocks of data "pages", the data from a file a "stream" and the file directory the "stream directory".
		In other words the pdb file is divided into blocks of 400h bytes (1,024 bytes in decimal).
	www.jorgon.freeserve.co.uk /Other/pdb.htm (2290 words)

	RCSB Protein Data Bank
		The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease.
		The RCSB is a member of the wwPDB whose mission is to ensure that the PDB archive remains an international resource with uniform data.
		In citing the PDB please refer to: H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne: The Protein Data Bank.
	beta.rcsb.org /pdb (320 words)

	PDB At A Glance (Site not responding. Last check: 2007-10-23)
		The PDB structure entries, consisting of a collection of files having nondescript names, cannot be easily grasped in a biochemically meaningful context.
		The PDB structures can be classified in a given context by searching the information in these fields using pre-defined search strings.
		PDB entries are listed in the context of secondary/tertiary structure in the "Structural Classification of Proteins (SCOP)" (Cambridge Univ.) WWW server.
	cmm.info.nih.gov /modeling/pdb_at_a_glance_about.html (471 words)

	Press-release: ACD and PDB
		Advanced Chemistry Development (ACD) and the Protein Data Bank (PDB) are proud to announce a collaboration in which ACD will provide their naming software product ACD/Name to the PDB for use in its data processing and annotation operations.
		Due to the size of the PDB and the complexity of the structures, the Name algorithm will be provided to the PDB in the form of ACD's IUPAC Name Batch software, capable of running on the SGI platform.
		The PDB is the authoritative worldwide data repository for the processing and distribution of 3-D biological macromolecular structure data and protein crystal structures, dating back to the very first structures ever solved by x-ray diffraction.
	www.acdlabs.com /clients/pr_pdb.html (568 words)

	Palm PDB Converter
		In fact, the ASCII form is designed to be more than just editable by humans; it's also easily editable by programs, provided the programs are written in a little language called Lua.
		The converter module supplies interpretations for the ``application info'' part of the PDB file, as well as an interpretation for the data in each ``record.'' The converter was written based on PDB documentation found at Road Coders.
		The remaining modules are used either for the common parts of the PDB format or as auxiliary stuff to help build new converters.
	www.eecs.harvard.edu /~nr/pilot/pdb (680 words)

	Help Using the PDB
		PDB files that contain atomic coordinates expanded to form the complete likely quaternary structure may be downloaded from these pages.
		Please note that although Rasmol is utilized by the PDB it is not PDB software and users are referred to the official Rasmol Web site for the most recent version and for more complete information.
		Obtaining Documentation on the PDB File Format The latest version of the PDB file format is available for browsing (frames version) and may be downloaded as a single HTML document or as a plain text document.
	dwb.unl.edu /Teacher/NSF/C08/C08Links/www.rcsb.org/pdb/pdb_help.html (1440 words)

	PDB File Internals > The Internal Structure of .pdb Files (Site not responding. Last check: 2007-10-23)
		Apparently, a PDB 1.00 format exists as well, but it seems to be structured quite differently.
		The PDB file's random-access structure borrowed from file systems allows addition and deletion of data with minimal effort, just like files can be modified with ease on a file system media.
		Now that the internal format of PDB files is clear, the next problem is to identify the contents of their streams.
	www.awprofessional.com /articles/article.asp?p=22685 (1863 words)

	Cracking PDB Symbol Files > Global PDB File Layout (Site not responding. Last check: 2007-10-23)
		This table is indispensable as soon as "holes" appear in the PDB file due to the rearrangement of streams.
		If a stream is rewritten to the end of the PDB file, releasing the pages it occupied before, the allocation bit table reflects that the previous pages are free while the new pages are in use.
		Most PDB files, such as the Windows 2000 symbol files and the debugging information generated by Microsoft Visual C/C++ 6.0, employ the 1-KB scheme, as depicted on the left side of Figure 1.
	www.informit.com /articles/article.asp?p=22429&seqNum=3 (1160 words)

	File Extension .PDB Details
		Insight II is a molecular modeling environment that provides a graphical interface to algorithms for molecular dynamics, homology modeling, de novo design, and electrostatics.
		PDB Converter is a Windows application that can create NSBasic for Palm-compatible PDB files interactively (by direct data entry into its spreadsheet) or by converting existing files in various formats.
		The PDB is the single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data.
	filext.com /detaillist.php?extdetail=PDB (840 words)

	PDB FILE FORMAT FAQ
		Although microheterogeneity does not present a problem within the coordinate records, it does introduce a difficulty in the specification of the sequence in the SEQRES records where only a single residue may be specified for each sequence position.
		Covalently bound ligands are assigned the chain identifier of the polymer chain to which the ligand is bound.
		In this example, a MHC class I molecule is complexed (not covalently bound) with a peptide from the gag protein of HIV2.
	pdb.rutgers.edu /format-faq-v1.html (2382 words)

	Kepware Technologies - iFIX PDB for Intellution
		The iFix PDB Settings tab contains fields that enable you to adjust the behavior between the processing of the iFix process database (PDB) tags and the server tags.
		This timeout can occur if the server is busy processing other requests, or if iFix PDB has lost communications with the server.
		In the case of lost communications, the iFix PDB will automatically re-establish communications with the server so that successive timeouts do not occur.
	www.kepware.com /Support_Center/iFIX_PDB.html (1103 words)

	PDB Format/UMass, Amherst (Site not responding. Last check: 2007-10-23)
		Below is a short overview of the components of PDB files used by RasMol.
		A graphic display of how the atoms are numbered in amino acids and nucleotides is available from U California San Francisco, PDB Atom Definitions.
		PDB files are plain text (ASCII) files made up of one-line, 80-character 'records'.
	www.umass.edu /microbio/rasmol/pdb.htm (404 words)

	Target PDB Monitor
		The PDB coverages of targets are calculated based on PDB biological macromolecular structure database and JCSG tracking and annotation database.
		The sequence alignmnet program BLAST from NCBI BLAST is used to search homologous sequences between targets and PDB sequences with Expect (Evalue cut-off) at 0.001 and at least 20 of aligned residues within target sequence.
		The PDB sequences and structure data are downloaded from PDB FTP server.
	www.jcsg.org /tpm/help/document.html (377 words)

	The not-so-secret presidential daily brief. - By Thomas Blanton - Slate Magazine (Site not responding. Last check: 2007-10-23)
		Because 10 PDBs from the Johnson administration are in the public domain, officially declassified by the U.S. government.
		The declassified PDBs contain such extraordinarily sensitive items as this one on Egypt: "Nasir, in a speech to the nation on Saturday, outlined a 'program of action' to bring about political reform.
		One of the PDBs is even published in the latest volume of the distinguished State Department documentary series Foreign Relations of the United States.
	slate.msn.com /id/2097476 (1110 words)

	VAST Help
		PDB: The four-character PDB-Identifier of the structure neighbor.
		Note that non-alphanumeric characters such as dashes, hyphens, underscores, etc. may be used as chain names by PDB.
		Domains are parsed based on geometrical criteria (the ratio of intradomain contacts to interdomain contacts) by an automatic method and can be visualized with Cn3D.
	www.ncbi.nlm.nih.gov /Structure/VAST/vasthelp.html (2170 words)

	RCSB Protein Data Bank
		The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease.
		The RCSB is a member of the wwPDB whose mission is to ensure that the PDB archive remains an international resource with uniform data.
		In citing the PDB please refer to: H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne: The Protein Data Bank.
	pdbbeta.rcsb.org /pdb (278 words)

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