Common File Formats. For Insight II Release December Scranton Road San Diego, CA / Fax: 619/

Transcription

1 Common File Formats For Insight II Release 98.0 December Scranton Road San Diego, CA / Fax: 619/

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3 Copyright * This document is copyright 1998, Molecular Simulations Incorporated. All rights reserved. Except as permitted under the United States Copyright Act of 1976, no part of this publication may be reproduced or distributed in any form or by any means or stored in a database retrieval system without the prior written permission of Molecular Simulations Inc. The software described in this document is furnished under a license and may be used or copied only in accordance with the terms of such license. Restricted Rights Legend Use, duplication, or disclosure by the Government is subject to restrictions as in subparagraph (c)(1)(ii) of the Rights in Technical Data and Computer Software clause at DFAR or subparagraphs (c)(1) and (2) of the Commercial Computer Software Restricted Rights clause at FAR , as applicable, and any successor rules and regulations. Trademark Acknowledgments Catalyst, Cerius 2, Discover, Insight II, and QUANTA are registered trademarks of Molecular Simulations Inc. Biograf, Biosym, Cerius, CHARMm, Open Force Field, NMRgraf, Polygraf, QMW, Quantum Mechanics Workbench, WebLab, and the Biosym, MSI, and Molecular Simulations marks are trademarks of Molecular Simulations Inc. Apex-3D is a trademark of DCL Systems International, Ltd. Felix and FTNMR are trademarks of Hare Research, Inc. IRIS, IRIX, and Silicon Graphics are trademarks of Silicon Graphics, Inc. ISIS and MACCS-3D are registered trademarks of MDL Information Systems, Inc. AIX, Risc System/6000, and IBM are registered trademarks of International Business Machines, Inc. UNIX is a registered trademark, licensed exclusively by X/Open Company, Ltd. PostScript is a trademark of Adobe Systems, Inc. The X-Window system is a trademark of the Massachusetts Institute of Technology. NSF is a trademark of Sun Microsystems, Inc. FLEXlm is a trademark of Highland Software, Inc. Permission to Reprint, Acknowledgments, and References Molecular Simulations usually grants permission to republish or reprint material copyrighted by Molecular Simulations, provided that requests are first received in writing and that the required copyright credit line is used. For information published in documentation, the format is Reprinted with permission from Document-name, Month Year, Molecular Simulations Inc., San Diego. For example: Reprinted with permission from Common File Formats for Insight II Release 9.80 Products, December 1998, Molecular Simulations Inc., San Diego. * U.S. version of Copyright Page

4 Requests should be submitted to MSI Scientific Support, either through electronic mail to or in writing to: MSI Scientific Support and Customer Service 9685 Scranton Road San Diego, CA To print photographs or files of computational results (figures and/or data) obtained using Molecular Simulations software, acknowledge the source in the format: Computational results obtained using software programs from Molecular Simulations Inc. dynamics calculations were done with the Discover program, using the CFF91 forcefield, ab initio calculations were done with the DMol program, and graphical displays were printed out from the Cerius 2 molecular modeling system. To reference a Molecular Simulations publication in another publication, no author should be specified and Molecular Simulations Inc. should be considered the publisher. For example: Common File Formats for Insight II Release 9.80 Products, December San Diego: Molecular Simulations Inc., 1998.

5 Table of Contents 1. Current File Formats 1 Version 98.0, December Sequence Alignment Files (.align) Sample.align File Cartesian Coordinate Archive File (.arc) Sample.arc File Cartesian Coordinate File (.car) File Header Coordinate Section Header Periodicity Records Coordinate Section Sample.car Files Output Coordinate File (.cor) Elements Data File (elements.dat) Comment Record Element Record Bond Record Free-Format Files (.frm) Fields Format Descriptions Fractional Coordinates Atom Creation vs. Referencing Existing Atoms Sample Free-Format Files Standard Graph Definition File (.grf) Sample Graph Definition File Hessian Files (.hessian,.hessianx,.xhessian) Sample.hessian FIle Dynamics Trajectory History Files (.his and.fhis) Special Information for the Discover 2.9.x Program Special Information for the Discover 98.0/3.0.0 Program45 Layout Template File (.ltpl) Sample Layout Template File Exclusion Shell File (.ludi_pseudo_protein, fort.12) Molecular Data File (.mdf) Header Record Insight II Common File Formats/December 1998 v

6 . Comment Record Topology Section Symmetry Section End Record Sample.mdf Files Molecular Structure File (.msf) Brookhaven Protein Databank File (.pdb) Reading PDB Files Writing PDB Files X-PLOR Coordinate File (.pdbx) NMR Peak Intensity/Integral (.pks) Description of Sections Sample.pks File Pseudoatom Library (.plb) Description of Sections Sample.plb File Proton Chemical Shifts (.ppm) Description of Sections Sample.ppm File Dynamics Scratch File (.pre) Protein Bond Angle Table (pro_angle.dat) Description of Sections Sample pro_angle.dat File Protein Bond Length Table (pro_bond.dat) Description of Sections Sample pro_bond.dat File NMR Project (.proj) Description of Sections Sample.proj File Insight Protein Miscellaneous Properties Table (pro_misc.dat) 82 Description of Sections Sample pro_misc.dat File X-PLOR Molecular Structure File (.psf) Residue Library (.rlb) Portion of Insight s Residue Library Version Number Header Card/First Line of a Residue Atom Cards/Second and Following Lines of a Residue90 Terminal Card/EOF Last Line of Residue Library Specific Format for Insight s Residue Library Distance, Torsion, Chiral, and NOE Volume Restraints (.rstrnt) 98 Description of Sections vi Insight II Common File Formats/December 1998

7 Sample.rstrnt File Residue Topology File (.rtf) Torsion File (.scs_tor) Format of the Torsion File Description of Sections Sample.scs_tor File Binary Torsion File (.xdr_tor) Structure Data File (.sd ) Amino Acid Sequence Files (.seq) Sample.seq File Subset Definition File (.sub) Sample Subset Definition File Table Files (.tab) Sample.tab File Graph Data Files (.tbl) Sample Graph Files User File (.usr) Classic File Formats 131 Cartesian Coordinate File (.car,.cor) Molecular Data File (.mdf) Format of the Molecular Data File Cartesian Coordinate Archive File (.arc) Insight II Common File Formats/December 1998 vii

8 . viii Insight II Common File Formats/December 1998

9 List of Tables 1. Release 97.0 File Formats and Their Modules Structure of a Cartesian Coordinate File for Systems Not Characterized by Helical Symmetry Structure of Cartesian Coordinate File Containing Helix Information Element Record Definition Bond Record Definition Field Type Format of.his File Format of.fhis File Structure of an.mdf File Types and Order of Atomic Data and Flag Settings Connectivity Record Items Types of Periodicity Default Values of axes Entries Atom Set Types Sections of.pks File Variables in.pks File Sections in.plb File Variables in.plb File Sections in.ppm File Variables in.ppm File Sections in pro_angle.dat File Variables in pro_angle.dat File Sections in pro_bond.dat File Variables in pro_bond.dat File Sections in.proj File Variables in.proj File Sections in pro_misc.dat File Insight II Common File Formats/December 1998 ix

10 . 28. Variables in pro_misc.dat File Keywords in pro_misc.dat File General Reference for Residue Names in Insight s Residue Library Greek Letter Notation Used in Insight s Residue Library for Residue Atom Names Torsion Angle Names Included in Insight s Residue Library Remote Prochiral Center Definition Chirality Restraints Definition Distance Restraints Definition NOE Distance Restraints Definition NOE Overlapped Distance Restraints Definitions NOE Overlapped Distance Restraints Definition Mixing Times Restraints Definition NOE Volume Restraints Definition NOE Volume Restraints Definition NOE Overlapped Volume Restraints Definition NMR Dihedral Restraints Definition J Dihedral Restraints Definition Amino Acid Single-Letter Codes Atom Record Definition Torsion Record Definition Pseudoatom Definition Pseudo Atom Set Definition x Insight II Common File Formats/December 1998

11 List of Tables 1. Release 98.0 File Formats and Their Modules Structure of a Cartesian Coordinate File for Systems Not Characterized by Helical Symmetry Structure of Cartesian Coordinate File Containing Helix Information Element Record Definition Bond Record Definition Field Type Format of.his File Format of.fhis File Structure of an.mdf File Types and Order of Atomic Data and Flag Settings Connectivity Record Items Types of Periodicity Default Values of axes Entries Atom Set Types Sections of.pks File Variables in.pks File Sections in.plb File Variables in.plb File Sections in.ppm File Variables in.ppm File Sections in pro_angle.dat File Variables in pro_angle.dat File Sections in pro_bond.dat File Variables in pro_bond.dat File Sections in.proj File Variables in.proj File Sections in pro_misc.dat File Insight II Common File Formats/December 1998 xi

12 . 28. Variables in pro_misc.dat File Keywords in pro_misc.dat File General Reference for Residue Names in Insight s Residue Library Greek Letter Notation Used in Insight s Residue Library for Residue Atom Names Torsion Angle Names Included in Insight s Residue Library Remote Prochiral Center Definition Chirality Restraints Definition Distance Restraints Definition NOE Distance Restraints Definition NOE Overlapped Distance Restraints Definitions NOE Overlapped Distance Restraints Definition Mixing Times Restraints Definition NOE Volume Restraints Definition NOE Volume Restraints Definition NOE Overlapped Volume Restraints Definition NMR Dihedral Restraints Definition J Dihedral Restraints Definition Amino Acid Single-Letter Codes Atom Record Definition Torsion Record Definition Pseudoatom Definition Pseudo Atom Set Definition xii Insight II Common File Formats/December 1998

13 1 Current File Formats Version 98.0, December 1998 This document describes the file formats used by more than one Insight II product or module in the 98.0 software release. The information is presented in alphabetical order, by filename extension, or by descriptive name where there is no mandatory filename extension. This book lists only the file formats that are used by more than one Insight II product or module. You should always look in the File Formats appendix of each product s user guide for information about formats that are unique to that product. The appendix of this book describes fixed, non-changing formats that were used by earlier versions of Insight II software and that can still be used. Each of these classic formats has a current version described in this main section of the book. Table 1 lists the products or modules that use the formats described in this book. Table 1. Release 98.0 File Formats and Their Modules format page modules align 3 Consensus, Homology arc 6 Insight II, Discover, others car 9 Insight II, Discover, others Insight II Common File Formats/December

14 1. Current File Formats Table 1. Release 98.0 File Formats and Their Modules format page modules cor 18 Insight II, Discover elements.dat 19 Insight II fhis 39 See his. frm 21 Insight II grf 33 Insight II hessian 37 Discover, DGII, DMol, Turbomole, Zindo hessianx 37 See hessian. his 39 Analysis, Decipher, Discover, Insight II ltpl 46 Insight II ludi_pseudo_protein 48 Ligand_Design mdf 48 Insight II, Discover, others msf 67 Insight II pdb 68 Insight II pdbx 69 X-PLOR pks 70 Felix, NMR_Refine plb 71 DGII, NMR_Refine ppm 74 Felix, NMR_Refine pre 75 Discover pro_angle.dat 75 Consensus, Homology, NMR_Refine, Xsight 2 Insight II Common File Formats/December 1998

15 Sequence Alignment Files (.align) Table 1. Release 98.0 File Formats and Their Modules format page modules pro_bond.dat 77 Consensus, Homology, NMR_Refine, Xsight proj 80 DGII, NMR_Refine pro_misc.dat 82 Consensus, Homology, NMR_Refine, Xsight psf 85 X-PLOR rlb 85 Insight II, Ligand_Design rstrnt 98 Consensus, Discover, Discover_3, Felix, NMR_ Refine rtf 110 Insight II, Modeler scs_tor 111 Analysis, Apex-3D, Decipher, Search_Compare sd 117 Analysis, Apex-3D, Converter seq 117 Consensus, Homology sub 118 Insight II tab 119 Insight II tbl 119 Insight II, Discover, others usr 128 Insight II xdr_tor 111 See scs_tor. xhessian 37 See hessian. Sequence Alignment Files (.align) Insight II Common File Formats/December

16 1. Current File Formats An alignment of two or more amino acid sequences can be read into Consensus or Homology from a.align file with the Get Sequences Alignment command. The filename should end in the extension.align, since only files with this extension are listed in the value-aid in the Get Sequences Alignment command. The file is a text file containing lines of no more than 1000 characters each. Shorter lines (typically 80 characters or less) can be used, if desired, to make the file easier to read and edit. Each line begins with a protein name (up to six characters long) followed by a colon ( : ). The remainder of the line contains the amino acid sequence of the named protein. In addition to the single-letter amino acid codes listed above, the sequence may contain gap characters ( - ) and break characters ( ); the latter indicate breaks between protein chains. The text lines are organized into blocks of lines, each block containing exactly one line for each protein in the alignment. Blocks are separated from one another by one or more blank lines; therefore no blank lines are allowed within a block. The proteins must be listed in the same order in all blocks in the file. The protein name must conform to the rules for object names in Insight II. This means that the name must contain only letters, digits, underscores ( _ ), and dollar signs ( $ ), and that the first character must be either a letter or a dollar sign. The Consensus program corrects an illegal protein name read from an alignment file if only the first character is illegal. If the first character is a digit or an underscore, but the second character is a letter or dollar sign, then the illegal first character is simply deleted from the name. If both the first and second characters are digits or underscores, then a leading dollar sign is prepended to the name. The colon at the end of each protein name can be followed by any number of space characters to separate the name from the sequence. In the first block these intervening spaces are used to establish the alignment of the N-termini of the sequences. Tab characters cannot be used for this purpose. In an alignment between a long sequence and a short sequence fragment, the shorter sequence might not span all blocks in the file. In such cases, each block not containing the shorter sequence must still have a line for that sequence; these place-holding lines contain only the name of the protein, terminated by a colon. Alignment files can also contain comments beginning with either a pound sign ( # ) or exclamation mark (! ). A comment can be 4 Insight II Common File Formats/December 1998

17 Sequence Alignment Files (.align) placed either on a line by itself or at the end of a line containing sequence information. Comments are completely ignored when the file is read. A line containing only a comment is not recognized as a blank line for the purpose of separating blocks of sequence lines. Sample.align File Here is an example of a sequence alignment in the correct format for an alignment file: # Comments like this one are completely ignored.! The exclamation mark also denotes a comment. # Note how leading space characters are used in the first # block to establish the proper alignment of the N- termini of # the four sequences. Also notice that a place-holding line # is required in the third block because the short sequence IER # does not extend that far. IER: mtqspsslsas-vgdrvtitcqas------qdiikylnwyqqtpgka PCM1: VMTQSPSSLSVSA-GERVTMSCKSSQSLLNSGNQKNFLAW- YQQKPGQP JBF: EIVLTQSPAITAASL-GQKVTITCSASSS VSSLHW- YQQKSGTS F91: IQMTQT-TSSLSASLGDRVTISCRASQD------ISNYLNWYQQK- PDGT IER: pklliyeasnlqagvpsrfsgsgsgtdytftisslqped PCM1: PKLLIYGASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCQN DHS JBF: PKPWIYEISKLASGVPARFSGSGSGTSYS- LTINTMEAEDAAIYYCQQWT- F91: VKLLVYYTSRLHSGVPSRFSGSGSGTDYS- LTISNLEHEDIATYFCQQGST IER: # place holder PCM1: YP-LTFGAGTKLEIKRADAAPTVSIFPPSSEQLTSGGAS JBF: YPLITFGAGTKLELKRADAAPTVSIFPPSSEQ F91: TP-RTFGGGTKLEIKRRADAAPTVSIFPPS Insight II Common File Formats/December

18 1. Current File Formats Cartesian Coordinate Archive File (.arc) The.arc file has the same format as the.car file (see Cartesian Coordinate File (.car) on page 6), with two exceptions. The first difference is that the.arc file may contain more than one coordinate header section. This means that an.arc file may contain multiple instances ( frames ) of the same molecular system. The second difference is that the.arc file is generally written as a single record, instead of a series of single records where each line of data contains a carriage return as the last character in the line. Two utilities are available for converting the single-record.arc file to a multiple record file and vice versa. The descriptions of the dirtoseq and seqtodir utilities are found in Part 1 of the Discover 2.9.x/98.0/3.0.0 online user documentation. The format is: File format line HELIX header line (if present) PBC header line title/energy line date line PBC record (if present) HELIX record for molecule A (if present) atom record for atom 1... atom record for atoms i end HELIX record for molecule B (if present) atom record for atom i atom record for atoms j end HELIX record for molecule C (if present) atom record for atom j Insight II Common File Formats/December 1998

19 Cartesian Coordinate Archive File (.arc). atom record for atoms k end... end end title/energy line date line PBC record (if present) HELIX record for molecule A (if present) atom record for atom 1... atom record for atoms i end HELIX record for molecule B (if present) atom record for atom i atom record for atoms j end HELIX record for molecule C (if present) atom record for atom j atom record for atoms k end... end end Insight II Common File Formats/December

20 1. Current File Formats Sample.arc File The example shows an.arc file for a 2D-periodic, helical system with three frames. Ordinarily, an.arc file consists of a single long line with no carriage returns. Carriage returns have been inserted into the following example to make it more understandable.!biosym archive 3 HELIX PBC=2D Frame 1!DATE Thu Jul 19 18:39: PBC (P 1) HELIX C ETHE 1 c3 C H ETHE 1 h H H ETHE 1 h H C ETHE 1 c2 C H ETHE 1 h H H ETHE 1 h H end HELIX C ETHE 1 c2 C F ETHE 1 f F H ETHE 1 h H C ETHE 1 c2 C H ETHE 1 h H H ETHE 1 h H end end Frame 2!DATE Thu Jul 19 18:39: PBC (P 1) HELIX C ETHE 1 c3 C H ETHE 1 h H H ETHE 1 h H C ETHE 1 c2 C H ETHE 1 h H H ETHE 1 h H end HELIX C ETHE 1 c2 C F ETHE 1 f F H ETHE 1 h H C ETHE 1 c2 C H ETHE 1 h H H ETHE 1 h H end end Frame 3!DATE Thu Jul 19 18:39: PBC (P 1) HELIX C ETHE 1 c3 C H ETHE 1 h H H ETHE 1 h H C ETHE 1 c2 C H ETHE 1 h H Insight II Common File Formats/December 1998

21 Cartesian Coordinate File (.car) H ETHE 1 h H end HELIX C ETHE 1 c2 C F ETHE 1 f F H ETHE 1 h H C ETHE 1 c2 C H ETHE 1 h H H ETHE 1 h H end Cartesian Coordinate File (.car) The.car file contains the Cartesian coordinates of a molecular system, as well as related positional information. This information is dynamic and can change during the course of a calculation. Note that.car files are used by several Insight II products; therefore, some of the information present may be ignored by some programs or used only by certain programs. In particular, the ability of the.car file to support helical and 2D periodic systems is accomplished by the presence of special lines that are present only if the.car file contains 2D periodic and/or helix information. This information is currently relevant only to the Polymer product, and in that context, only to the Discover 98.0/3.0.0 program. In addition, since the Discover program does not handle infinite helices, it does not read.car files containing helix information. If a.car file contains 2D periodicity without helix information, however, the Discover 98.0/3.0.0 program (but not the Discover 2.9.x program) can read it and can also write files for these systems. There are several differences between the file format described in the Discover and Insight documentation and the format presented here, to enable atom names, potential types, and residue names to be longer than in previous versions. The.car file consists of one file header (which includes statements indicating what kinds of information are present in the file), one coordinate section header, optional 2D or 3D periodicity records, one coordinate section for each molecule in the file, and one endof-file statement. All lines in the file are exactly 80 characters long. The coordinate section(s) includes: 1. Optional helix record. Insight II Common File Formats/December

22 1. Current File Formats 2. Atom records. 3. End-of-section statement. The overall structure of a.car file for nonhelical systems is shown in Table 2 and that of a file containing helix information is shown in Table 2. Descriptions and examples of the major parts follow. The Insight and Polymer documentation explains the orientation of the various axes and angles referred to in the.car file description. Finally, examples of.car files for several kinds of systems are shown. Table 2. Structure of a Cartesian Coordinate File for Systems Not Characterized by Helical Symmetry (Page 1 of 2) NOTE: Information relating to 2D periodicity is indicated by bold type; italic type indicates contents that are replaced by real data; plain type indicates actual contents. Coordinate conventions are described in the Insight and Polymer documentation. line columns contents comments First:!BIOSYM archive 3 Second: PBC=ON, PBC=OFF, PBC=2D one of these three choices must be present The coordinate header begins with the third line: Third: 1 64 title for the system if available this line may be blank but must energy be present Fourth:! DATE day month date time year or just!date Fifth line: PBC information if PBC=ON: 1 3 PBC 4 13 a cell vector a in angstroms b cell vector b in angstroms c cell vector c in angstroms alpha cell angle α in degrees beta cell angle β in degrees gamma cell angle γ in degrees space group name Fifth line: PBC information if PBC=2D: 1 3 PBC 4 13 k plane vector k in angstroms 10 Insight II Common File Formats/December 1998

23 Cartesian Coordinate File (.car) Table 2. Structure of a Cartesian Coordinate File for Systems Not Characterized by Helical Symmetry (Page 2 of 2) NOTE: Information relating to 2D periodicity is indicated by bold type; italic type indicates contents that are replaced by real data; plain type indicates actual contents. Coordinate conventions are described in the Insight and Polymer documentation. line columns contents comments l plane vector l in angstroms gamma plane angle γ in degrees plane group name Sixth Nth (This section is repeated for each molecule in the system.): 1 5 atom name 7 20 x Cartesian coordinate of in angstroms atom y Cartesian coordinate of in angstroms atom z Cartesian coordinate of in angstroms atom type of residue containing atom residue sequence name relative to beginning of current molecule, left justified potential type of atom left justified element symbol partial charge on atom Final line for a given molecule: 1 3 end Final line for the entire molecular system input: 1 3 end File Header The first record of a.car file must be:!biosym archive # The! must be the first character in the file. The Discover program interprets this line as indicating an ASCII file containing coordinate records as outlined in this section. The string archive indicates that the contents of the file are those of a.car file; the # Insight II Common File Formats/December

24 1. Current File Formats Table 3. Structure of Cartesian Coordinate File Containing Helix Information (Page 1 of 2) NOTE: Information relating to helices and 2D periodicity is indicated by bold type; italic type indicates contents that are replaced by real data; plain type indicates actual contents. Coordinate conventions are described in the Insight and Polymer documentation. PBC=2D can be read by the Discover 98.0/3.0.0 program but not the Discover 2.9.x program. line columns contents comments First:!BIOSYM archive 3 Second: HELIX Third: PBC=OFF, PBC=2D one of these two choices must be present The coordinate header begins with the fourth line: Fourth: 1 64 title for the system if available this line may be blank but energy must be present Fifth: 1! DATE day month date time year or just!date Sixth line: PBC information if PBC=2D: 1 3 PBC 4 13 k plane vector k in angstroms l plane vector l in angstroms gamma plane angle γ in degrees plane group name Seventh (This helix record is part of the section that repeats for each molecule in the system.): 1 5 HELIX 6 15 sigma in degrees d in angstroms kappa angle between l axis and helix axis in degrees lambda angle between k axis and helix axis in degrees Tk fractional position of helix axis along k axis Tl fractional position of helix axis along l axis Eighth Nth (This section repeats for each molecule in the system.): 1 5 atom name 7 20 x Cartesian coordinate of atom in angstroms y Cartesian coordinate of atom in angstroms z Cartesian coordinate of atom in angstroms type of residue containing atom 12 Insight II Common File Formats/December 1998

25 Cartesian Coordinate File (.car) Table 3. Structure of Cartesian Coordinate File Containing Helix Information (Page 2 of 2) NOTE: Information relating to helices and 2D periodicity is indicated by bold type; italic type indicates contents that are replaced by real data; plain type indicates actual contents. Coordinate conventions are described in the Insight and Polymer documentation. PBC=2D can be read by the Discover 98.0/3.0.0 program but not the Discover 2.9.x program. line columns contents comments residue sequence name relative to beginning of current molecule, left justified potential type of atom left justified element symbol partial charge on atom Final line for a given molecule: 1 3 end Final line for the entire molecular system input: 1 3 end identifies the file format. For example, 3 indicates that the file format is as specified here for the Discover program, versions 2.9.5/ 3.2 and later. If helix information is not present in the.car file, then the second line indicates whether the file contains PBC information. If helix information is present, then the second line of the.car file consists of the word HELIX and the third line indicates whether the file contains PBC information. Note that helical symmetry is not currently compatible with 3D periodicity. So if the second line is HELIX and PBC=ON is found, an error message is generated. Valid file headers:!biosym archive 3 HELIX PBC=2D!BIOSYM archive 3 HELIX PBC=OFF!BIOSYM archive 3 PBC=ON Insight II Common File Formats/December

26 1. Current File Formats!BIOSYM archive 3 PBC=OFF!BIOSYM archive 3 PBC=2D Coordinate Section Header The coordinate section header consists of two lines. Both lines must be present in the.car file. The first line, which may be blank, usually contains a title and the energy. The second line must contain the characters!date, optionally followed by the full date when the file was written (see Tables 2 and 2). Periodicity Records A periodicity record is present in the.car file only if the entry PBC=ON or PBC=2D is present in the file header. For 3D periodicity, indicated by the file header line PBC=ON, the PBC section is the same for the Insight and Discover programs (see Table 2). This line contains the word PBC, followed by the a, b, and c unit cell lengths, the values of the α, β, and γ angles, and the space group name. Please see the Discover 2.9.x/98.0/3.0.0 User Guide for a discussion of valid space group names. For 2D periodicity, indicated by the file header line PBC=2D, the PBC section (Tables 2 and 2) contains the word PBC, the k and l values, the value of γ, and the plane group name. These coordinates are explained in the Insight and Polymer documentation. Currently, only the (P1) plane group is supported, and only the Discover 98.0/3.0.0 program (not the Discover 2.9.x program) reads such files. Example PBC record for 2D periodicity: PBC (P 1) Coordinate Section Coordinate records are present for each molecule in the system, so this section is repeated as a whole for each molecule. 14 Insight II Common File Formats/December 1998

27 Cartesian Coordinate File (.car) Helix Records If any helix information is present in a.car file, the second line of the file must be the word HELIX. If a molecule has helical symmetry (i.e., it is an infinite helix), then an extra line is present in the relevant coordinate section, just before the atom records for that molecule. Note that each helical molecule has its own helix record. The new line in the coordinate section contains the word HELIX, followed by the σ and d values, the κ and λ angles, and the Tk and Tl positions (see Table 2). These coordinates are explained in the Insight and Polymer documentation. Example helix record: HELIX Atom Records The atom records (see Table 2) contain information that identifies the complete Insight name of each real atom, some general properties of the atom, and its location in 3D space. Ghost atoms are generated from real ones according to symmetry and periodicity information (see, for example, Periodic Boundary Conditions, in the Discover 2.9.x/98.0/3.0.0 User Guide). End Records The coordinate section for each molecule in the system must end with the word end in the first three columns of the last line of the section. In addition, the entire file must end with the word end, also in the first three columns of the last line of the file. Sample.car Files The following examples indicate the correct format for.car files (although the data are not necessarily physical). The underlined row of numbers at the top of each file simply indicates column numbers they are not part of a.car file. Insight II Common File Formats/December

28 1. Current File Formats Example 1: Nonperiodic, Nonhelical System !BIOSYM archive 3 PBC=OFF!DATE Thu Jul 19 18:39: C ETHE 1 c2 C H ETHE 1 h H H ETHE 1 h H C ETHE 1 c2 C H ETHE 1 h H H ETHE 1 h H end C ETHE 1 c2 C H ETHE 1 h H H ETHE 1 h H C ETHE 1 c2 C H ETHE 1 h H H ETHE 1 h H end end Example 2: 3D-Periodic, Nonhelical System !BIOSYM archive 3 PBC=ON!DATE Thu Jul 19 18:39: PBC (P 1) C ETHE 1 c2 C H ETHE 1 h H H ETHE 1 h H C ETHE 1 c2 C H ETHE 1 h H H ETHE 1 h H end C ETHE 1 c2 C H ETHE 1 h H H ETHE 1 h H C ETHE 1 c2 C H ETHE 1 h H H ETHE 1 h H end end Example 3: 2D-Periodic, Nonhelical System These files are not read by the Discover 2.9.x program, but are read by the Discover 98.0/3.0.0 program Insight II Common File Formats/December 1998

29 Cartesian Coordinate File (.car)!biosym archive 3 PBC=2D!DATE Thu Jul 19 18:39: PBC (P 1) C ETHE 1 c2 C H ETHE 1 h H H ETHE 1 h H C ETHE 1 c2 C H ETHE 1 h H H ETHE 1 h H end C ETHE 1 c2 C H ETHE 1 h H H ETHE 1 h H C ETHE 1 c2 C H ETHE 1 h H H ETHE 1 h H end end Example 4: Nonperiodic, Helical System !BIOSYM archive 3 HELIX PBC=OFF!DATE Thu Jul 19 18:39: HELIX C ETHE 1 c2 C H ETHE 1 h H H ETHE 1 h H C ETHE 1 c2 C H ETHE 1 h H H ETHE 1 h H end HELIX C ETHE 1 c2 C H ETHE 1 h H H ETHE 1 h H C ETHE 1 c2 C H ETHE 1 h H H ETHE 1 h H end end Example 5: 2D-Periodic, Helical System These files are not read by the Discover 2.9.x program, but are read by the Discover 98.0/3.0.0 program. Insight II Common File Formats/December

30 1. Current File Formats !BIOSYM archive 3 HELIX PBC=2D!DATE Thu Jul 19 18:39: PBC (P 1) HELIX C ETHE 1 c2 C H ETHE 1 h H H ETHE 1 h H C ETHE 1 c2 C H ETHE 1 h H H ETHE 1 h H end HELIX C ETHE 1 c2 C H ETHE 1 h H H ETHE 1 h H C ETHE 1 c2 C H ETHE 1 h H H ETHE 1 h H end end Output Coordinate File (.cor) The output coordinate file is automatically output at the end of a Discover 2.9.x minimization run and contains the minimized set of coordinates for the system. However, if you want to output a.cor file with the Discover 98.0/3.0.0 program, you must specify it with the writefile or the Analyze/Output command (see the Discover 2.9.x/98.0/3.0.0 User Guide). If you want to continue a minimization from the point at which a previous minimization finished, then rename the output.cor file to an input.car file before performing the minimization. Alternatively, the.cor file name can be specified in the begin command (see the Discover 2.9.x/98.0/3.0.0 User Guide for versions 2.9.x and 98.0/3.0.0, respectively, of the Discover program). The format of the.cor file is identical to that of the.car file. 18 Insight II Common File Formats/December 1998

31 Elements Data File (elements.dat) Elements Data File (elements.dat) The elements data file (elements.dat) is used by Insight II to retrieve various types of information about the periodic table elements. The data file contains the values for van der Waals and covalent radii; minimum, maximum, and common valences; and atomic weights for all the elements supported by Insight II. The data file also contains the bond lengths for bonds between different elements. There are three kinds of record types in the element data file: 1. Comment Record 2. Element Record 3. Bond Record Comment Record Comment lines begin with a # and may occur anywhere in the file. Example: # code vdw radius cov. radius min val max val common weight Element Record Element records contain the various type of information about the elements (Table 4). Table 4. Element Record Definition Contents element element code vdw radius Comment Record identifier One or two letter element name van der Waals radius of the element Insight II Common File Formats/December

32 1. Current File Formats Table 4. Element Record Definition Contents covalent radius minimum valence maximum valence common valence atomic weight Comment Covalent radius of the element Minimum number of bonds allowed for the element Maximum number of bonds allowed for the element Number of bonds in the most common state Atomic weight of the element Example: element H element C element N Bond Record The bond record specifies the bond lengths between various elements. All the bond records must come after the element records. The bond lengths for all lone pairs are assumed to be 1.1 Å. Table 5. Bond Record Definition Contents bond element code element code bond length Comment Record identifier One- or two-letter element name One- or two-letter element name Bond length in angstroms Example: bond H N 1.03 bond C C 1.54 bond C O 1.43 bond L S Insight II Common File Formats/December 1998

33 Free-Format Files (.frm) Free-Format Files (.frm) Free-format files, with the.frm extension, should be stored in and used from the $BIOSYM/data/insight directory. If you do not have write permission in this directory, you can setenv $INSIGHT_DATA to another location before you start up Insight. Format files consist of sequentially executed commands from the set described below. All but the FORMAT and BOND_TABLE commands are a single line. The commands in the group beginning FORMAT_ are followed by any number of field specifiers and terminated by an END_FORMAT command. All commands and field specifiers must appear exactly as listed here; no abbreviations or lower case letters are allowed. IGNORE_FOR number On input: Skip the given number of lines. Useful for skipping a fixed length header section (a line of the header can be read as the TITLE field). On output: No function on output. IGNORE_TO [start] string On input: Skip lines until a line is encountered which contains the given string. The optional start parameter may be used to indicate in what column testing for the match should begin, or may be * to check for a match anywhere in the line. Note that column numbering begins at 1 for the leftmost column. If no start column is supplied, matching begins in column 1. This command might be used to get down to the ATOM section of a pdb file. On output: No function on output. IGNORE_WHILE [start] string On input: Skip lines while they match the string given. The optional start parameter functions as in IGNORE_TO. On output: No function on output. Insight II Common File Formats/December

34 1. Current File Formats MARKER [start] string On input: Skip one line from the input file On output: Output the given string starting in the column specified or column 1 if no start is given. An asterisk (*) given for the start column is interpreted as column 1 in this command. Used for such things as END markers that separate atom and connectivity sections of the file. FORMAT_FOR number On input: Read the specified number of lines using the format that follows. The number field is often a symbolic variable such as $NUM_ATOMS filled by an earlier read. On output: Write the specified number of lines using the given format. When fields corresponding to atom data are included, the data come from the list of specified atoms starting at the beginning and advancing one atom each time the format is applied. If a symbolic variable like $NUM_ATOMS is used, then it is evaluated to the number of atoms in the object specified in the put command. FORMAT_TO [start] string On input: Read input lines using the format until a line containing the given string is encountered. The line with the matching string is not processed. This type of read can be used in conjunction with the MARKER command for files with sections separated by markers such as END. On output: Write out the information in the format for every atom specified in the put command. FORMAT_WHILE [start] string On input Read input lines until encountering a line whose initial characters do not match the given string. Stops so that this non-matching line is the next line to be read. This type of read is designed for pdbstyle files where sections are delimited by different keywords. The length and presence of the string does not affect the columns of the format specification. 22 Insight II Common File Formats/December 1998

35 Free-Format Files (.frm) On output: Write out the information in the format for every atom in the list. The string does not automatically appear in the line being written but may be output using a MARKER field in the format. FORMAT_TO_EOF On input: Read input lines using the format until the end of the input file is encountered. This type of read should be the last in a format description file, since all subsequent reads will fail. On output: Write out the information in the format for every atom in the list. END_FORMAT On input: On output: Marks end of a format specification. Marks end of a format specification. BIDIRECTIONAL_BONDS On input: Lets the system know that all bonds are listed twice, once in each direction. Insight.mdf files use this convention. On output: Lets the system know that all bonds are listed twice, once in each direction. Insight.mdf files use this convention. Fields Fields are described by a keyword corresponding to some piece of information about the atom or molecule, a start position in the input line where this information is found, and a field length indicating how many characters are to be read/written for this field. The start position and/or field length may be an asterisk indicating space/comma-delimited fields. Floating-point fields such as ATOM_X may have an optional number of decimal places in their length specifier. The format is length.decimal_length. The regular field types are described in Table 6. Insight II Common File Formats/December