------------------------------------------------------------------------
Protein Data Bank
Quarterly Newsletter
Release #71 
January 1995


------------------------------------------------------------------------
The latest version of the Electronic Deposition Form should be obtained 
from the FTP /pub directory before depositing data.

------------------------------------------------------------------------

January 1995 PDB Release

    3091 full-release atomic coordinate entries
         (174 new additions

    2869 proteins, enzymes, and viruses
     212 nucleic acids
      10 carbohydrates

     368 structure factor entries
      31 NMR experimental entries

The total size of the atomic coordinate entry database
is 1003 Mbytes uncompressed.


------------------------------------------------------------------------
What is New at the PDB

During December 1994, the number of entries in the PDB passed the 3,000 
mark and has now reached 3,091. The number of entries continues to rise 
exponentially with a 75 percent increase in the size of the PDB in 1994 
alone. In parallel, the number of accesses to PDB over the Internet has 
been increasing as shown in the number of FTP downloads per month. This 
is equivalent to one download in each minute of every day ­ and it 
doesn't include the number of entries downloaded via the WWW!

To make network access easier, the PDB Browser has been modified so 
that it now runs on WWW client viewers such as Mosaic and is accessible 
through the PDB's HTML home page (http://www.pdb.bnl.gov/). This is 
described in the article `PDB Announces a WWW Version of the PDB 
Browser'. See also M.C. Peitsch, T.N.C. Wells, D.R. Stampf, and 
J.L. Sussman, TIBS 20, 82-84 (1995).

In parallel with our efforts at Brookhaven, a number of outside groups 
have created and developed tools that add enormously to the value of 
the data in the PDB, by examining them from different points of view. 
One such project is SCOP: a Structural Classification of Proteins 
Database for the Investigation of Sequences and Structures developed 
at the MRC Laboratory of Molecular Biology and the Cambridge Centre
for Protein Engineering. This project is further described in a 
separate article. We encourage groups who have been developing programs
or tools to extract various kinds of information from the PDB for their 
own requirements, or which may be of general use, to send a description 
of this to the PDB (newsletter@pdb.pdb.bnl.gov). We will try to provide 
brief articles in this Newsletter, post them on our Listserver, and 
where appropriate, insert hyperlinks in our Mosaic HTML home page.

PDB intends to introduce significant changes to the format of the
ATOM/HETATM records. Please pay particular attention to the article
`PDB Proposes Changes to ATOM/HETATM Records` describing these
changes ­ your input is valued.

Users who are interested in receiving future printed copies of the PDB 
Newsletter should note that our mailing list is being re-initialized
following the distribution of this issue. Please see the following 
article for additional information.

                                                  ­ Joel L. Sussman



------------------------------------------------------------------------
Newsletter Distribution Changes

In view of the ease of retrieving the Newsletter via Internet (FTP, 
Gopher, and WWW from the subdirectory /newsletter in PostScript and 
ASCII formats), the distribution of large numbers of printed Newsletters 
through the postal system seems quite wasteful, especially in this era 
of tight budgets. Therefore, the PDB is re-initializing the Newsletter 
mailing list following the distribution of this issue.

Current subscribers, as well as new subscribers, who wish to receive 
printed copies of future Newsletters must contact us immediately.
A Newsletter Request Form is available in the file news_mailinglist
from the FTP /pub directory. This form may be completed and returned 
electronically (send_news@pdb.pdb.bnl.gov) or via the postal system 
(PDB Newsletter Mailing List, Chemistry Department, Building 555, 
Brookhaven National Laboratory, Upton, NY 11973 USA).


------------------------------------------------------------------------
PDB Proposes Changes to ATOM/HETATM Records

PDB is planning a change in format of the ATOM and HETATM records. This 
modification addresses needs brought to our attention by many users. If 
acceptable, this change will take place in approximately two to three 
months. Along with other changes to our format, as discussed in the 
article `Revised PDB Format Description', these changes are part of 
our current efforts to produce PDB entries using CIF.

PDB will introduce this format change in such a way as to minimize 
negative impact on existing software. Numerous applications rely on 
the current coordinate record format, and we wish to give ample notice 
of this change. We need input from the community regarding this issue,
so please examine the proposal carefully and send us your comments 
(abola1@bnl.gov).

PDB proposes to use columns 73 - 76 to identify specific segments of the 
molecule, and columns 77 - 80 to provide element information. Currently, 
columns 71 - 80 contain the entry's ID code and line number. If 
elimination of these data presents a problem to any programs, we need to 
be informed.

Columns 73 - 76 will contain the segment id (SEGID), which will 
identify specific segments of molecules. The segment can consist 
of a complete chain or a portion of a chain. The importance of this 
new field can be readily understood if one considers an antibody 
structure having two molecules in the asymmetric unit. Since each 
chain must have a unique chain identifier, the two heavy chains and 
two light chains cannot currently be labeled to indicate their nature. 
SEGID's of CH, VH1, VH2, VH3, CL, and VL would clearly identify 
regions of the chains and the relationship between them. Users of 
X-PLOR will be familiar with SEGID as used in the refinement 
application of X-PLOR.

SEGID is defined as a string of at most four (4) alphanumeric 
characters, left justified, and can include a white space, e.g., 
CH86, A 1, NASE.

Columns 77 - 78 will contain the atom's element symbol, right 
justified, and columns 79 - 80 will indicate any charge on the 
atom, e.g., MN2+,O1-, H. In the past, hydrogen naming sometimes
conflicted with IUPAC conventions. For example, we have not been 
able to label a hydrogen HG11, but as 1HG1 in order for it not 
to be confused with mercury. After adopting the format change, 
HG11 will be allowed in columns 13 - 16, and hydrogen will be 
clearly identified in columns 77 - 78, thus columns 13 - 16 
will continue to be used to uniquely identify each atom.

Please send your comments on these proposed changes to ATOM 
and HETATM records to Enrique Abola (abola1@bnl.gov). Again,
if acceptable to our users, these changes will be implemented 
in approximately two to three months.


------------------------------------------------------------------------
PDB Release Policy

To clarify PDB's policy regarding on-hold entries, the following is 
included in the acknowledgment letter sent to depositors upon data 
acceptance:

	PDB follows the IUCr guidelines which state that 
	coordinates may be held (before release) no longer 
	than one (1) year and structure factors may be held 
	no longer than four (4) years from the date of publication. 
	PDB has chosen to apply the same guidelines to NMR 
	restraints data, allowing a maximum hold of four (4) years. 
	Requests that the PDB delay release of your data 
	(put it on hold) should be submitted at the time 
	of the initial deposition. PDB cannot consider hold 
	requests received more than one week after the date 
	of this acknowledgment letter. A one-time extension 
	of up to six (6) months due to delay in publication 
	can be requested in writing. In no case will a coordinate 
	data set be held for longer than eighteen (18) months 
	from the date of deposition. Deposition of data constitutes 
	your acceptance of PDB's Release Policy. 

	Please note that information on the status of all entries, 
	including those on hold, is available to the public. The 
	PDB Pending and Waiting list, updated daily, is available 
	through anonymous FTP and is searchable using WWW and Gopher. 
	This file gives the status, including hold expiration date 
	if the entry is on hold, of every pending entry. In addition, 
	the full list of on-hold entries, with their hold expiration 
	dates, is available via FTP, WWW, and Gopher. See the file 
	named /pub/on_hold.list.


------------------------------------------------------------------------
Revised PDB Format Description

The revised PDB Format Description for Atomic Coordinate Entries has 
been recently released. The purpose of this document is to completely 
describe the contents of PDB coordinate entry files. Several changes 
are being introduced to PDB files to make them more explicit to the 
human reader and more easily computer-parseable. Additionally, once 
the macromolecular CIF has been adopted, these changes will pave 
the way for conversion to CIF.

An important enhancement to the current PDB format is in ATOM/HETATM 
records (see article `PDB Proposes Changes to ATOM/HETATM Records`). 
Additions to PDB files include new record types, such as TITLE, CAVEAT, 
KEYWRD, CISPRO, MODRES, DBREF, and SEQADV; introduction of keyword:value 
pairs in certain records such as COMPND, SOURCE, and REMARK 3; further 
detailing of the heterogen groups with the new records HETNAM, HETSYN, 
and HETSIT (list of residues in very close proximity to a given 
heterogen); the deprecation of footnotes; and restructuring of some 
REMARK records to make them more machine-accessible.

This revised Format Description will be helpful to several communities. 
It will assist depositors in preparing entries for deposition, guide 
software and information resource developers, and help users of the PDB 
understand the contents of coordinate entries. Ultimately, this document 
and the enhanced entry format will facilitate the conversion of PDB 
files into CIF.

This document is available in several formats (HTML, plain text, and 
PostScript) from FTP, Gopher, and WWW in the /pub directory. A more 
advanced HyperText version is being designed for later release.

A convenient way to peruse the Format Description is to use Mosaic or 
another WWW interface. Access the PDB home page by opening the URL 
http://www.pdb.bnl.gov/. Move to "PDB Format Description" where you'll
see several choices, including:

    -  Table of Contents
         Advances you to the pertinent page of the document.

    -  The Format Description Document
         Brings up the entire document.

    -  Keyword Search of The Format Description
         Allows you to locate a specific word within the document.

A sample page from the revised PDB Format Description follows:

CRYST1

Overview:

The CRYST1 records present the unit cell parameters, space group, and Z 
value. This record is present even if the structure was not determined 
by crystallographic means, in which case it simply defines a unit cube.

Record Format:

	COLUMNS	    DATA TYPE	       FIELD	     DEFINITION

	 1 -  6	     Record name      "CRYST1" 
	 7 - 15	     Real	      a	             a (Angstroms)
	16 - 24	     Real	      b	             b (Angstroms)
	25 - 33	     Real	      c	             c (Angstroms)
	34 - 40	     Real	      alpha	     alpha (degrees)
	41 - 47	     Real	      beta	     beta (degrees)
	48 - 54	     Real	      gamma	     gamma (degrees)
	56 - 66	     LString(11)      sGroup	     Space group
	67 - 70	     Integer	      z	             Z-value

Details:

    -  If the coordinate entry describes a structure determined by a 
       technique other than crystallography, CRYST1 will contain 
       a=b=c=1.0, alpha=beta=gamma=90, space group P 1, and z=1.

    -  The Z-value is the number of polymeric chains in a unit cell. 
       In the case of heteropolymers, Z is the number of occurrences 
       of the most populous chain.

    -  As an example, given two chains A and B, each with a different 
       sequence, and the space group P 2 that has 2 equipoints in the 
       standard unit cell, the following table gives the correct 
       Z-value.


	Asymmetric Unit Content	     Z-value

	         A	                2
	         AA	                4
	         AB	                2
	         AAB	                4
	         AABB	                4

Verification/Validation/Value Control Authority:

The given space group and Z-values are checked during processing for
correctness and internal consistency. The calculated SCALE is compared 
to that supplied by the depositor. Packing is also computed, and close 
contacts of symmetry-related molecules are diagnosed.

Relationships to Other Record Types:

The unit cell parameters are used to calculate SCALE. If the EXPDTA 
record is NMR, FIBER DIFFRACTION, or THEORETICAL MODEL, the CRYST1 
record is predefined as a=b=c=1.0, alpha= beta=gamma=90, space group 
P 1, and z=1. In these cases, an explanatory REMARK will also appear 
in the entry.

Deposition Form Section and Prompt:

CRYSTAL (CRYST1)
a (A)	:
b (A)	:
c (A)	:
alpha (deg)    :
beta  (deg)    :
gamma (deg)    :
space group    :
space group number	:

Z-value	:

Text to explain unusual unit-cell data	        :
Symmetry operations for non-standard setting	:

CIF Equivalent:

From the core CIF Dictionary:
-----------------------------

data_cell_[]
;	Data items in the _cell_ category record details about 
        the crystallographic cell parameters.
;

data_cell_angle_ 
	loop_ _name	  '_cell_angle_alpha'
	                  '_cell_angle_beta'
	                  '_cell_angle_gamma'
data_cell_formula_units_Z
data_cell_length_
	loop_ _name	  '_cell_length_a'
	                  '_cell_length_b'
	                  '_cell_length_c'
data_cell_special_details
data_cell_volume
	 _definition

Examples:

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
CRYST1   52.000   58.600   61.900  90.00  90.00  90.00 P 21 21 21    8
CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1
======================================================================


------------------------------------------------------------------------

PDB Announces a WWW Version of the PDB Browser

Previous Newsletter articles described a GUI-based browser utility 
running under tcl/tk for searching the PDB archives. This browser 
provided the ability to search text portions of entries using arbitrary 
regular expressions. Additionally, the browser incorporated graphical 
tools such as RASMOL and MidasPlus to view selected molecules. The 
browser was written in a modular fashion, permitting replacement of 
the search, front-end, or display mechanisms.

Recently, a WWW version of the browser was made available to the user 
community (http://www.pdb.bnl.gov/cgi-bin/browse). This replaces the 
front end of the browser with popular WWW viewer programs such as 
Mosaic or Netscape. The WWW front end provides most of the 
functionality of the original browser while adding the following 
benefits:

    -  All searching and access is over the network. One need not 
       install Perl, tcl, and tk. (But on general principles, 
       you should!)

    -  The archive being searched is the up-to-date PDB (or a 
       mirrored copy!)

    -  Hypertext links are provided in the PDB file display to the 
       Enzyme Data Bank as well as to the sequence databases.

    -  Hypertext links are provided to use the default display program 
       (e.g., RasMol) and pictures from M. Peitsch.

    -  PDB access is provided for PC, Macintosh, and Unix computers.

The primary drawback is that the search of the remark fields has been 
deleted due to the time necessary to complete the searches and the 
network time-outs that resulted.

Short-term plans include replacing search scripts with a SYBASE 
database engine, increasing linkages to sequence and reference 
databases, and taking advantage of video and audio capabilities
of WWW. Exporting of the server source code to PDBSA Affiliated 
Centers, permitting the user community to take advantage of the
best network links available, is taking place.


---------------------------------------------------------------------
NMR Depositors

PDB would like to remind depositors of NMR entries including 
multiple models that all models should be presented in a common 
aligned orientation corresponding to the alignment shown in any 
related publications.


---------------------------------------------------------------------
Use Care When Depositing Data

Occasionally a new set of coordinates received at PDB contains 
errors in the data. For example, we may find an atom distant from 
the rest of its residue. Sometimes we find that errors have been 
introduced by a depositor doing last-minute hand-editing of the 
data. We recommend that depositors do a final check of each 
coordinate file immediately before sending it to the PDB.

In addition, authors should carefully check the proposed entry 
that we send them, and consider all points mentioned in our 
accompanying letter.

Viewing the molecule on a graphics terminal also may help in 
detecting errors.


------------------------------------------------------------------------
SCOP: a Structural Classification of Proteins Database for the 
Investigation of Sequences and Structures

    This article was written by Alexey G. Murzin, 
    Steven E. Brenner, Tim Hubbard, and Cyrus Chothia, 
    MRC Laboratory of Molecular Biology and Cambridge 
    Centre for Protein Engineering, Hills Road, 
    Cambridge CB2 2QH, England. It describes a database 
    that complements the PDB and should be of interest 
    to the user community.

Presently, the PDB contains 3091 entries and the number is increasing 
by about seventy-five per month. To facilitate the understanding of, 
and access to, this information, we have constructed the Structural 
Classification of Proteins (SCOP) database. This database provides 
a detailed and comprehensive description of the structural and 
evolutionary relationships of proteins whose three-dimensional 
structures have been determined. It includes all proteins in the
current version of the PDB and many proteins whose structures have
been published but whose coordinates are not available from the PDB.

The classification of the proteins, or the individual domains in the
case of large proteins, is on hierarchical levels that embody the
following evolutionary and structural relationships:

    -  Family
         Proteins are clustered together into families on the basis 
         of clear evidence for their having a common evolutionary 
         origin.

    -  Superfamily
	 Families whose proteins have low sequence identities but 
         whose structures and functional features suggest that
         a common evolutionary origin is probable are placed 
         together in superfamilies.

    -  Common Fold
         Superfamilies and families are defined as having a
         common fold if their proteins have same major secondary
         structures in the same arrangement and with the same 
         topological connections.

    -  Class
         For the convenience of users, the different folds have
         been grouped into classes. Most of the folds are
         assigned to the All-alpha, All-beta, alpha and beta, 
         or alpha plus beta classes.

Each entry (for which coordinates are available) has links to 
images of the structure, interactive molecular viewers, the 
atomic coordinates, sequence data, homologues, and MEDLINE 
abstracts. Two major searching facilities are currently available. 
Homology searching permits users to enter a sequence and obtain 
a list of structures which have significant levels of sequence 
similarity. Keyword searching finds matches from both the text 
of the SCOP database and the headers of PDB structure files. 
The SCOP database is available as a set of tightly coupled 
hypertext pages on WWW. This allows it to be accessed by any 
machine on the Internet (including Macintoshes, PCs, and 
workstations) using free WWW reader programs, such as Mosaic. 
Once such a program has been started, it is necessary only to 
open URL http://scop.mrc-lmb.cam.ac.uk/scop/ to obtain the home 
page of the database.

The SCOP database was originally created as a tool for understanding 
protein evolution through sequence-structure relationships and 
determining if new sequences and new structures are related to 
previously known protein structures. In a more general way, the 
highest levels of classification provide an overview of the 
diversity of protein structures now known, and would be appropriate 
both for researchers and students. The specific lower levels should 
be helpful for comparing individual structures with their evolutionary 
and structurally-related counterparts. In addition, the search 
capabilities with their easy access to data and images make SCOP 
a powerful general-purpose interface to the PDB.

For comments or additional information, please contact Steven Brenner 
(scop@www.bio.cam.ac.uk).


------------------------------------------------------------------------
The EBI NetNews Filtering Service

    This article was written by Jose R. Valverde 
    and Rob Harper, European Bioinformatics 
    Institute, an EMBL Outstation, Hinxton Hall, 
    Hinxton, Cambridge CB10 1RQ, England. It 
    describes one way to access Usenet News 
    that may be of interest to users who are 
    overwhelmed with the information available.

Usenet News is possibly the most popular tool used today by researchers 
for efficient communication. It provides fast dissemination of news, 
fast on-line help, and a free forum for scientific discussion. However, 
the newsgroups either tend to be too specialized for interdisciplinary 
research (thus requiring a scientist to follow many groups), or they 
address too broad an interest (which results in information overload).

The NetNews Filtering Service provides an easy way in which researchers 
can filter newsgroups automatically so that they will only receive those 
articles in which they are interested. A user can define one or several 
independent profiles that describe his or her fields of interest by means 
of keywords. The server will then periodically check the profiles against 
all the newsgroups in Bionet, EMBnet, and Sci and select only those 
articles that best reflect the interests of the user. The filter makes 
a preliminary review and selects a small number of articles, and, if 
the user finds any of these especially interesting, the server can be 
instructed to mail the full contents.

The EBI NetNews Filtering Service can be accessed in either of two ways: 
giving commands by e-mail or through an easy graphical user interface 
using a WWW client (e.g., NCSA Mosaic). In the first case a user can 
start by sending an e-mail message to netnews@ebi.ac.uk with no subject 
and a body consisting of a single line with the word `help'. Working 
with Mosaic or another WWW browser, a user can select the URL 
http://www.ebi.ac.uk which will connect to our server and then select 
`Documentation Software and Services' from the main menu. In both cases 
the user can get on-line help, look at examples, and make tests before 
subscribing.

For comments or additional information, please contact Jose R. Valverde 
(Jose.Valverde@ebi.ac.uk).


------------------------------------------------------------------------
MakeMolS

    This article was written by Liisa Holm, European 
    Molecular Biology Laboratory, Heidelberg, Germany. 
    It describes a tool that may be of interest to a 
    wide cross section of PDB users.

MakeMolS is a simple tool to facilitate the generation of input 
scripts to MolScript [P. Kraulis, J. Appl. Cryst. 24, 946-950 (1991)], 
a popular program for creating molecular graphics in PostScript form. 
MolScript supports a variety of representations of protein structures, 
including Jane Richardson-type schematic ribbon drawings to highlight 
secondary structure elements. The sole functionality of MakeMolS is 
to read the secondary structure definitions from a DSSP file 
[W. Kabsch and C. Sander, Dictionary of Protein Secondary 
Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical 
Features. Biopolymers 22, 2577-2637 (1983)] and write them out 
in the form of MolScript instructions for a ribbon drawing. 
The DSSP program and database are available from the URL 
http://www.sander.embl-heidelberg.de/dssp/ and from anonymous 
FTP (ftp.embl-heidelberg.de) in the following directories: 
/pub/databases/protein_extras/dssp and /pub/software/unix/dssp. 
The Fortran source code of MakeMolS may be obtained from the PDB 
FTP directory /pub/program_tape/makemols.f. The user may further 
modify the scripts in a text editor to exploit the full spectrum
of options provided by MolScript.

For comments or additional information, please contact Liisa Holm 
(HOLM@embl-heidelberg.de).


------------------------------------------------------------------------
ZINC - Galvanizing CIF to Work with Unix 

The July 1994 Newsletter described the basic structure of a CIF 
(Crystallographic Information File), the standard that will probably 
become the interchange format of the future for the PDB due to 
increased amounts of information that it can contain. It was also 
pointed out that those who are accustomed to working with the PDB 
format in a Unix environment (with grep, awk, perl, diff, etc.) 
will not be able to use those skills in dealing directly with CIF.

This article describes a format called ZINC (Zinc Is Not CIF) which is 
fully accessible to Unix tools, and a number of utilities that allow a 
CIF to be converted into a ZINC and back again, as well as versions of 
some familiar Unix tools (grep, diff) and some surprising new tools 
(zincSubset and zincNl) that should make access to CIF much easier.

What is the Problem with CIF in a Unix Environment?

CIF defines a format that is generally at odds with Unix tools.

    -  Many Unix tools are line oriented ­ they expect related 
       information to be on a single line whereas CIF allows 
       and encourages the use of multiple lines, both by 
       limiting the line length and in the definition of 
       loops.

    -  Many Unix tools break the lines into fields based on 
       a separator character. Both PDB and CIF formats work 
       against this, the former by having column-based fields, 
       the latter by encouraging the liberal use of white space 
       (across line boundaries).

    -  A number of Unix tools treat the information in files 
       as being position dependent (diff, head, tail, etc.). 
       The PDB file format adapted neatly to this, but CIF allows 
       a much wider variation in the placement of data.

­ ZINC

Zinc is not an interchange format as CIF is, but rather a piping 
format, i.e., a format that makes the contents of a CIF accessible 
to Unix utilities. Each data line of a ZINC file consists of five 
tab-separated fields:

	block	name	index	value	loop-id

The first field is the name of the CIF data block (the data_ prefix 
is omitted) and is repeated on each line where appropriate. The second 
field is the name of the data item. The third field is an index 
specifier, which is empty for non-looped data, and is a zero-based 
index for looped data. The fourth field is the data item itself. 
For multiple-line CIF data, new line characters are replaced by the 
two characters \n. The backslash character becomes the escape 
character throughout the ZINC format. The fifth field is a loop 
identifier. Comments that appear in a CIF are associated with 
the previous token and are also represented in the ZINC format.

­ Existing Tools

A number of tools have been developed to support the user community in 
using the ZINC format and to access the information contained in a CIF. 
Most are simple and allow users to modify the code to tackle new prob
lems. Source is provided for all.

    -  cifZinc, obviously the first required tool, converts an existing 
       CIF into a ZINC. This is a C program that converts even the 
       largest CIF in a few seconds.

    -  zincCif, the next most important tool, takes a ZINC and creates a 
       pretty-printed CIF. Very often the pipeline:

                      cifZinc old.cif | zincCif > new.cif

       will produce a better looking CIF than the original.

    -  zincGrep, greps a ZINC (or a CIF file specified as a 
       command-line argument) for a regular expression and 
       returns the block name, data name, index, and value 
       of the match. This is the single most requested 
       tool for dealing with CIF.

    -  cifdiff is a four-line C-shell script that takes two 
       CIFs and determines the differences between them. It 
       will handle CIFs that have been rearranged, and even 
       loops with rearranged columns, and provide only the 
       real differences.

    -  zb, a small (< 200 lines) tcl/tk program that provides 
       a simple GUI front end to a ZINC or CIF, allows users 
       to browse through the contents. Multiple files as well 
       as multiple data blocks can be viewed simultaneously on 
       any X terminal. zb recognizes command-line argument 
       file names in the form *.cif as being a CIF and converts 
       t to a ZINC automatically.

    -  zincSubset is another C-Shell script that is very short 
       but very useful. It allows users to generate a custom 
       subset of any ZINC (CIF), simply by listing the data 
       blocks and data names that he or she wishes to include. 
       For example, if you wanted to extract only the names and 
       definitions from the mmCIF dictionary, you would create a 
       file (e.g., defs) with two lines that appear as:

	                    _name
	                    _definition

       (preceded and followed by tabs) and run the command:

                zincSubset defs mmcif94 | zincCif

    -  zincNl, a perl script, takes a ZINC file and creates a 
       Fortran compatible namelist file allowing easy access 
       to any CIF by Fortran programs without the need for 
       extensive I/O libraries or reprogramming. As with zb 
       above, it will automatically convert a CIF to a ZINC. 
       It may be used in the following pipeline which extracts 
       the coordinates from a CIF and presents them to a Fortran 
       program via the namelist mechanism:

            zincSubset coords datafile | zincNl | myfortran

       (where coords is a file that simply has three lines with 
       x, y, and z surrounded by tabs).

­ A Sample CIF and ZINC

The following CIF illustrates most aspects involved in translating to a 
ZINC:

#
#	A simple CIF
#

data_object

#
#	polygon
#
	_name
;
triangle
;
    loop_
 	_x _y
 	0.0	0.0
	1.0	0.0
	0.0	1.0

	_num_sides 3

In ZINC, this would appear as:

		(	    0	   #
		(	    1	   # 	  A simple CIF
		(	    2	   #
object		(	    3	   #
object		(	    4	   # 	  polygon
object		(	    5	   #
object		_name		   ;\ntriangle\n;
object		_x	    0	   0.0		           _x
object		_y	    0	   0.0	                   _x
object		_x	    1	   1.0	                   _x
object		_y	    1	   0.0	                   _x
object		_x	    2	   0.0	                   _x
object		_y	    2	   1.0	                   _x
object		_num_sides	   3

Note that comments `belong' to a data block and are represented with 
an open parenthesis for the data name. Initially, the data block name 
is defined to be the null string.

­ Code

The formal definitions of ZINC and the above mentioned 
programs are available from PDB using FTP, Gopher, or WWW 
(ftp://pub/other-software/Zinc). Please give it a try. 
All are invited to submit their favorite scripts that use 
ZINC. Any comments should be directed to Dave Stampf 
(drs@bnl.gov).


------------------------------------------------------------------------
Mirroring

Earlier this year, PDB started updating the FTP server with fully-
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Fortunately, a public domain package called mirror exists that does 
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and performs all necessary tasks needed to make them equivalent. We 
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the members of our user community who maintain complete local archives 
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If you wish to try this, here is what you need to do:

0)  Think: Decide what your local archive will look like. Will it be 
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1)  Prepare: Set up your local archive from a 1994 version of the 
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	mkdir /usr/distr    or where you want the files to go

	cd /CDROM/distr	    or where you are copying the files from


	    tar cf - . | (cd /usr/distr; tar xvf -)

2)  Get mirror: Copy the mirror software from PDB or elsewhere
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3)  Configure: Adapt a copy of the mirror.defaults configuration 
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4)  TEST!!! If you run mirror -n it will tell you what it will 
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5)  When you are satisfied, make the mirror run as part of your 
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As the mirror README says, `Objects in the mirror are closer than 
they appear!'


------------------------------------------------------------------------
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*Osaka University
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