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| |
| | 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). |
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http://www.jorgon.freeserve.co.uk/Other/pdb.htm
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| |
| | PDB Format/UMass, Amherst |
| | Below is a short overview of the components of PDB files used by RasMol. | | | PDB files are plain text (ASCII) files made up of one-line, 80-character 'records'. | | | PDB files also contain many other kinds of information. |
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http://www.umass.edu/microbio/rasmol/pdb.htm
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| | PDB and HDF5 Compared |
| | PDB code was found to be more succinct than HDF5 for similar operations, though HDF5 Lite has taken on the task of developing a simpler interface to HDF5. | | | 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. | | | PDB manages much of the data-type and data-space complexity by allowing the user to embed the information in the read or write call itself. |
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http://pact.llnl.gov/benchmarks.html
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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. | | | The PDB browser is used to provide an organized view and uniform frontend to inspect different objects related to planning problems, for example, domains, problems, axioms, facts, operators and sessions. | | | PDB evolved as a way of presenting this information in a graphical format in order to make these tasks easier. |
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http://www.cs.washington.edu/ai/pdb/pdb.html
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| |
| | PDB At A Glance |
| | This classification is based on the presence or absence of the words "complex", "inhibitor", or "activator" in the "COMPND" or "HEADER" fields of the PDB files. | | | The PDB structures can be classified in a given context by searching the information in these fields using pre-defined search strings. | | | The descriptive information in the PDB files is distributed between a set of fields (e.g. |
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http://cmm.info.nih.gov/modeling/pdb_at_a_glance_about.html
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| |
| | PDB Converter |
| | 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 can read HanDBase PDB files as well as NSBasic™ PDB files with string data, and will fill the spreadsheet with the records and their individual fields. | | | Note that PDB Converter will read the Creator ID, PDB type, and PDB Name from the PDB header when PDB files are read. |
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http://www.mverive.com/pdbconverter.htm
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| |
| | PDB Lite |
| | Technical information not needed by PDB Lite users, such as crystallographic properties, is omitted from the results. | | | The above PDB Lite sites were keeping their databases up to date with new releases when checked on. | | | However, at the present time, SearchLite does not incorporate several features of PDB Lite designed for occasional or nonspecialist users, such as students and most educators. |
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http://www.umass.edu/microbio/rasmol/pdblite.htm
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| |
| | pdb Documentation |
| | pdb would consider "foo" to have no data, the data pointer for this node would be set to NULL. | | | struct pdb* dbptr = pdb_load(NULL); /* * Assume this database structure is completely empty (this is evident because * NULL was passed to pdb_load() for the file name), it has nothing in it. | | | Determine if it has been X seconds since the last disk write of the specified database, and if the database requires a write due to a change; both of these conditions must be met for this function to return 1. |
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http://pdatabase.sourceforge.net
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| |
| | Module Documentation - Palm::PDB 1.8 |
| | It takes $pdb's AppInfo block, $pdb->{appinfo}, and returns a string of binary data that can be written to the database file. | | | It takes $pdb's sort block, $pdb->{sort}, and returns a string of raw data that can be written to the database file. | | | ParseSortBlock() should parse this data and return it, typically in the form of a reference to an object or to an anonymous hash. |
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http://aspn.activestate.com/ASPN/CodeDoc/p5-Palm/Palm/PDB.html
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| |
| | Cracking PDB Symbol Files |
| | 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. | | | The PDB header always occupies the first file page, and is followed by one or more pages containing the allocation bits. | | | 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. |
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http://www.informit.com/articles/article.asp?p=22429&seqNum=3
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| |
| | PDB At A Glance |
| | PDB At A Glance is a hypertext-based classification of the | | | Please read the PDB At A Glance description for important information. |
|
http://cmm.info.nih.gov/modeling/pdb_at_a_glance.html
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| |
| | D.W. Fearn - PDB Passive Direct Box Instructions |
| | In that case, use the input pad feature of the preamp (on the VT-1 or VT-2, use the -20 input position). | | | In many situations, there will be no difference in the switch position and it can be set either way. | | | These instructions are also available as a PDF file. |
|
http://www.dwfearn.com/pdbman.html
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| |
| | Dictionary Resources |
| | PDB data processing, data exchange, annotation, and database management operations all make heavy use of the data format and the content of the PDB Exchange Dictionary. | | | A complete list of PDB software tools for managing PDB data in mmCIF format can be found here. | | | The Protein Data Bank (PDB) uses macromolecular Crystallographic Information File (mmCIF) data dictionaries to describe the information content of PDB entries. |
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http://mmcif.pdb.org/index.html
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| |
| | MMTSB - All-atom Modeling: PDB File Manipulation |
| | If PDB files that were generated for or by CHARMM19 need to be read by | | | This is most useful for assembling a complex from different PDB files. | | | will ignore segment IDs when reading PDB files because PDB files from other sources may contain other information in the segment ID columns which might lead to confusion with CHARMM. |
|
http://mmtsb.scripps.edu/software/tutorial/allatom-pdbfiles.html
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| |
| | ProteinScope LE - Free viewer for Protein Data Bank PDB files |
| | The generated file is a 640 x 480 24 bit BMP that can be converted to other file formats, resized, or inserted directly in a PowerPoint presentation. | | | The PDB file is stored in a special folder PDBCache under ProteinScope LE. | | | Files can also be opened by dragging and dropping on to the ProteinScope window, or double clicking a PDB file if you select that file association. |
|
http://www.proteinscope.com/helpLE.htm
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| |
| | chapter9 |
| | A typical PDB file contains a header with information about the entry, literature references, as well as additional remarks that may contain information about how the protein was crystallised, the resolution and so on... | | | A partial example of PDB file is given below; parts removed are signalled by (...). | | | The first six columns are reserved for a keyword describing the type of information that follows on the line (such as HEADER, JRNL, REMARK, ATOM, HETATM, and so on). |
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http://swissmodel.expasy.org/course/text/chapte11.htm
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| |
| | PDB Lite: Find Macromolecules |
| | Questions on using PDB Lite may be sent to the PDB Help Desk, esther@darwin.bu.edu (Esther Epstein). |
|
http://www.pdb.bu.edu/oca-bin/pdblite
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| |
| | PDB Format Guide, Part 9 |
| | The PDB plans to be prudent and deliberate in making changes to the current PDB files in order to minimize the need to change existing programs. | | | When a change is made to PDB format, the format version number, as found in the entry and in this Contents Guide, will be incremented to the next whole number. | | | Beginning January 1997, the format of all PDB entries will be compliant with the current version of this Contents Guide. |
|
http://www.bmsc.washington.edu/CrystaLinks/man/pdb/part_8.html
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| |
| | Press-release: ACD and PDB |
| | 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 has agreed to add systematic names of small molecules to the Data Bank by using ACD's Name algorithm. | | | "At RCSB, we strive to add new value to the content of the PDB. |
|
http://www.acdlabs.com/clients/pr_pdb.html
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| |
| | 11.1 Creating additional PDB files: writepdb |
| | Before the PDB files are written, the user will be asked three questions. | | | The user might use this to see if there is any inter-penetration of symmetry mates. | | | PDB files for higher-dimensional (greater than 6D) minima |
|
http://www.caam.rice.edu/~djamrog/Somore/OnlineManual/node33.html
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| |
| | jaybaz [MS] WebLog : PDB always |
| | One drawback to creating PDB files with release builds in VS.NET is that when you enable "Generate Debugging Information" in the project settings, you get a non-optimized build regardless of the optimization setting. | | | In VC++6.0, even that data was moved into the PDB file, and only a ~100byte header entry that pointed to the.PDB file remained | | | Another concern I’ve heard is that accidentally deployed PDBs might be a security risk – that the extra information exposed could give away information useful to a hacker. |
|
http://blogs.msdn.com/jaybaz_ms/archive/2004/06/29/169024.aspx
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| |
| | PDB question |
| | from the PDB files; the binaries must be the same as were running on the user system | | | I have a couple of questions regarding using a PDB file. | | | Is there a way to force it to load a PDB you know is valid but it doesn't |
|
http://www.dotnetmonster.com/Uwe/ForumPost.aspx?article=vs-net-debugging:1295:u52peEy9EHA.2196@TK2MSFTNGP14.phx.gbl
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| |
| | The Washington Monthly |
| | And this whole idea that Ari is spinning, that the CIA might be less forthcoming in the PDBs in the future as a result of releasing this one, is just the purest horse twaddle. | | | The high level of classification is undoubtedly because all PDBs get this classification. | | | Surprisingly little was redacted from this document considering it was " eyes only " - the highest degree of publicly known security classification. |
|
http://www.washingtonmonthly.com/archives/individual/2004_04/003675.php
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| |
| | Archive of obsolete PDB entries |
| | The result of all queries and the links in the browsing pages will graphically display the "history" of all versions of the PDB entry as well as a textual comparison of the key features of the structure. | | | This archive can be used to locate and analyse obsolete entries from the Protein Data Bank (PDB). | | | Use the form field above to query the archive. |
|
http://pdbobs.sdsc.edu
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| |
| | PDBs for Biochemistry: Classical Proteins |
| | The contents of PDB are in the public domain, but it is expected that the authors of an entry as well as the PDB be properly cited whenever their work is referred. | | | The PDB files on this page were obtained from the Protein Data Bank, and were created by the authors listed above. | | | The following is the current citation for the PDB: |
|
http://chemistry.gsu.edu/glactone/PDB/Proteins/Classic/classic.html
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| |
| | ProteinScope PDB Viewer |
| | PDB files downloaded this way are stored in the ProteinScope\PDBCache folder for future reference. | | | Saving snapshots and videos of PDB files with ProteinScope is done with the toolbar icons or from the File menu: | | | The PDB file will load over the internet. |
|
http://www.proteinscope.com/phelp.htm
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| |
| | SWBIC - Searches of PDB |
| | [San Diego Supercomputing Center] "The PDB through Microsoft Windows, or WPDB for short, is a Microsoft Windows 3.1, Windows95, and Windows NT (client and server) based program to interrogate the 3-dimensional structure of biological macromolecules as found in the Protein Data Bank (PDB) using query and display tools like those shown above. | | | The results are collected and evaluated using automated model assessment programs. | | | The Live Bench Project is a continuous benchmarking program. |
|
http://www.swbic.org/links/1.12.2.php
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| |
| | Saving PDB to Disk |
| | By default, Windows hides "file extensions" from you, which makes it impossible to be sure you have named a PDB file correctly so that programs like RasMol or Chime can use it. | | | This is optional: If you want RasMol to start when you click on the PDB file, and if you know how to use a signature-changing utility program, change the PDB file's signature to TEXT/RSML. | | | The name must end in ".pdb" in order to work easily with common visualization software (e.g. |
|
http://pdb.ccdc.cam.ac.uk/oca-docs/litesave.html?v1=1hho
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| |
| | PDB - Palm DataBase, Program DataBase |
| | The molecules described by the files are usually viewed locally by dedicated software, but can sometimes be visualised on the world wide web. | | | More information about the definition of PDB may appear below: | | | 2) PDB is also derived from Program DataBase |
|
http://www.auditmypc.com/acronym/PDB.asp
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| |
| | Listings for PDB Heterogens and Their Codes |
| | From this page you can access files containing 'CONECT' records for PDB heterogens taken from the PDB 'Het Group Dictionary' and atomic coordinate files for PDB heterogens taken from the file hetero.pdb created by Gerard J. Kleywegt. | | | PDB Heterogen Listings Derived from the File hetero.pdb | | | These topology files have been created by Gerard Kleywegt. |
|
http://www.bmrb.wisc.edu/elec_dep/pdb_het_library/pdbhet.htm
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| |
| | The Command Post - 2004 US Presidential Election - Text of Released PDB |
| | Of the current intel (2 items) action was being taken as far as the PDB states that action is being taken. | | | Documents are classified for good reasons, including the need to allow officials to think through possibilities and decisions without second-guessing. | | | Posted by: bananas at April 13, 2004 08:29 AM Another thought about this PDB: |
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http://www.command-post.org/2004/2_archives/011534.html
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| |
| | PDB Mode for (X)emacs |
| | XEmacs and/or GNU Emacs are available for most computing platforms. | | | pdb-mode is an emacs-lisp minor mode for Emacs to perform a number of useful editing functions on Protein DataBank (PDB) formatted files. | | | The PDB mode functions are accessible from the PDB menu on the menu bar and also the right-mouse-click menu (CTRL-right-mouse in GNU Emacs). |
|
http://stein.bioch.dundee.ac.uk/~charlie/scripts/pdb-mode.html
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| |
| | PDBs for Biochemistry |
| | We have accumulated many PDB files which we feel will be useful in teaching undergraduate Biochemistry. | | | More information about PDB files can be found in the FAQ section. | | | One of the best PDB viewers is a program called RasMol. |
|
http://chemistry.gsu.edu/glactone/PDB/pdb.html
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| |
| | PDB Files |
| | The PDB files can be directly viewed by (a helper application) | | | To get the last version of Mage for Windows look at Duke-BioChem FTP and for other information about Mage to Mage Home Page. | | | There exists also an interface for Windows (ZIP) - you will need also Babel for DOS. |
|
http://vlado.fmf.uni-lj.si/pub/networks/pajek/data/pdbs.htm
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| |
| | [No title] |
| | GIF PDB2MGIF PDB2MULTIGIF PDB2 animated gif PDB to GIF PDB to MultiGIF PDB to animated GIF chemical software molecular modeling rendering software rotating melecules molecular vizualisation dekstop publishing chemical converter converter software imaging programa. | | | If you do not have a PDB file look at our example pages. | | | Solution: Use the [BROWSE] option to select a file. |
|
http://www.dkfz-heidelberg.de/spec/pdb2mgif/d1.html
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| |
| | PDB FILE FORMAT FAQ |
| | The information in this document has been gathered from the PDB Contents Guide document originally created at Brookhaven National Laboratory, a careful study of existing files, an RCSB Workshop held in October 1998, and discussion with many users of the data. | | | In this example Vitamin B6 complex, three-letter code PLP, is covalently bound to LYS A NZ. | | | Residues modeled as ALA due to lack of side chain density are relabeled to match the SEQRES. |
|
http://pdb.rutgers.edu/format-faq-v1.html
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| |
| | List of molecular graphics files (.PDB Index) |
| | ORTEP3 for Windows, this can display a variety of file formats, including PDB files. | | | Prof Eric Martz has an extensive set of notes and tutorials and these pages are an excellent starting point if you are considering developing your own web pages featuring molecular displays. | | | To see how CHIME and our JCAMP-DX viewer can be used for displaying spectra and molecular graphics with links between the two, see these examples. |
|
http://wwwchem.uwimona.edu.jm:1104/spectra/PDBIndex.html
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| |
| | PDB.C Source File |
| | buf[13],resname[5],atomname[5]; 00296 FILE *infile; 00297 PDBAtom *pdb; 00298 00299 | | | // print the PDB file out to a given file name | | | "memory allocation failed in main of test PDB class" |
|
http://www.ks.uiuc.edu/Research/namd/doxygen/PDB_8C-source.html
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| |
| | Enzyme Structures Database |
| | There are currently 10208 PDB-enzyme entries in the PDB (as at 28 March 2003) involving 9873 separate PDB files - some files having more than one E.C. number associated with them. | | | A new version of this database can now be found at:- | | | - Summaries and structural analyses of PDB data files |
|
http://www.biochem.ucl.ac.uk/bsm/enzymes/index.html
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| |
| | PHP Classes - Class: pDB |
| | pDB is a collection of PHP classes that implement a file based embeddable SQL database engine. | | | Main resource for pDB related files and docs. | | | It was written in pure PHP and does not require any special extension or external resource. |
|
http://www.phpclasses.org/browse/package/1672.html
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| |
| | VAST Help |
| | One may search for a possible neighbor that is not displayed in the current page. | | | Click on the Identifier to switch to the MMDB Summary page of the respective neighbor. | | | High number of heterogens contained in the PDB entry |
|
http://www.ncbi.nlm.nih.gov/Structure/VAST/vasthelp.html
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| |
| | PDB2VRML - PDB to VRML converter. |
| | The final goal is to write a representation of the molecular structure in the VRML format. | | | The PDB2VRML class allows the creation of objects which can read molecular structures stored in the PDB format. | | | Reads all atoms and connects from the given PDB file. |
|
http://www.realitydiluted.com/mirrors/reality.sgi.com/horstv_basel/pdb2vrml
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| |
| | RCSB Software Tools |
| | CIFTr -- A tool for translating mmCIF data files into PDB format | | | ADIT (for workstation) -- A web-based package for preparing, editing and checking structure data entries | | | OOSTAR -- Applications to Manipulate STAR Files (Objective-C) OpenRasMol -- Open source versions of RasMol (with CIF support) |
|
http://sw-tools.pdb.org
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| |
| | August 6 PDB |
| | The only recent information concerning possible current activities in the PDB related to two incidents. | | | Q: What information does this PDB item contain? | | | Q: Why has information been redacted from the PDB? |
|
http://www.agonist.org/annex/pdb.htm
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| |
| | GPCRDB 3D information |
| | The PDB identifiers are linked to PDB Structure Explorer (RCSB), the PDBREPORT database (outputs of the WHAT CHECK Structure Analysis) and Summary of PDB Structure (PDBsum). | | | 131 available PDB files (131 from the Swiss-Prot entries, 0 unrelated PDB entries) | | | PDB identifiers are extracted from the database cross-reference lines of the Swiss-Prot entries, the PDB databank, and the literature. |
|
http://www.gpcr.org/7tm/struct
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| |
| | PDB Viewer - Fast and Simple 3D Protein Viewer |
| | Many features I wanted to add were beyond the scope of this project, but I hope to have improved on some of the features present when compared to other PDB viewing packages. | | | Download the Windows version HERE, zipped with winzip | | | PDB Viewer is a simple Protein Data Bank Viewer for Windows and Linux written while I was at The University of Manchester. |
|
http://www.geocities.com/pdbviewer
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| |
| | D.W. Fearn PDB Passive Direct Box |
| | The output is 150 ohms, balanced, at mic-level. | | | The PDB Passive Direct Box is available from selected |
|
http://www.dwfearn.com/pdb.htm
|
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| |
| | File Extension Details for .PDB |
| | These are notes that might apply to a wide number of entries in the database. | | | Please use this association data with that in mind. | | | WinBackup 2.0 Standard will help you backup your PDB files and other valuable data in minutes! |
|
http://filext.com/detaillist.php?extdetail=PDB
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