Subject: DGEOM95

From: [email-masked] (Jeff Blaney)
Date: Wed, 8 Mar 95 18:11:14 -0800

DGEOM95 is now available from QCPE ([email-masked]).  DGEOM95 is
a  distance  geometry  program  for molecular model-building, receptor
modeling,   conformational   analysis,   and  NMR  solution  structure
determination.  DGEOM95's authors are:  Jeffrey M.  Blaney, Gordon  M.
Crippen, Andrew Dearing, J.  Scott Dixon, and David C.  Spellmeyer.

A copy of the release  notes  (relative  to  the  1990
release of DGEOM) is attached (2 pages).

Jeff Blaney
Chiron
[email-masked]

     DGEOM95 Release Notes	                                March, 1995
     
     New Features
     ------------

     *  Partial  metrization algorithm improves random sampling (Kuszewski,
     J., Nilges, M.,  Brunger, A.  T.  "Sampling and efficiency  of  metric
     matrix distance geometry:  A novel partial metrization  algorithm", J.
     Biomol.  NMR 1992, 2, 33-56).
     
     *  New  lower bound error function improves convergence (Havel, T.  F.
     "An   Evaluation   of    Computational   Strategies  for  Use  in  the
     Determination of Protein Structure from Distance Constraints  Obtained
     by Nuclear Magnetic Resonance", Prog.  Biophys.  Molec.  Biol.   1991,
     56, 43-78).
     
     *  Molecular  dynamics  has  been  added  as  a  refinement  method to
     supplement conjugate gradient  minimization.
     
     *  Random  coordinate  generation  has been added as an alternative to
     embedding.
     
     *  Automatic  connectivity generation and double bond assignment (even
     for conjugated  and aromatic systems).  This eliminates the  need  for
     supplying  CONECT records and/or editing them  to specify double bonds
     for most  organic  structures,  including  peptides  and  nucleotides.
     Automatic  connectivity generation will be performed if CONECT records
     are missing.
     
     *  Free-format  input  for  CONSTRAINT  and  ORIENT  files.  Backwards
     compatible with original version, except that now a  '*'  is  required
     for molecule and residue wildcards to mark their fields (previously, a
     blank  was  used).  Original DGEOM 1990  fixed-format constraint files
     will still work.
     
     *  Free-format  input  of  van  der Waals and covalent bond radii (the
     latter are needed for  connectivity generation).   DGEOM95  preassigns
     van  der  Waals and covalent bond radii only for C, N,  O, S, P, H, F,
     Cl, Br, I, and Du (dummy atom, radius = 0.).
     
     *  'REJECT'  rejects similar structures.  'REJECT' rejects the current
     structure if its minimum  RMSD to all previously  accepted  structures
     is  less  than  REJECT's  threshold  (default = 1.0  angstrom).   This
     ensures that all output structures will have a minimum pairwise RMSD >
     REJECT's threshold.
     
     *  New rules to detect conjugated groups (e.g.  butadiene, aniline, or
     phenol-like systems which  have restricted rotation about  the  single
     bond)  and  constrain  them  to be nearly coplanar (+/- 40   degrees);
     disulfide  and  hydrazine  torsions  are  constrained  to  be  +/-  90
     degrees.  Recognizes  thioamides and thioesters.
     
     *  Read  atom  names  beginning with integers and residue numbers with
     optional chain  identifiers from PDB format files.  
     
     *  New  'FLOAT'  command  available in CONSTRAINTS file for specifying
     chiral centers that can  racemize  or  'float',  and  amide  or  ester
     carbonyl carbons that should randomly sample cis and trans.
     
     *  Warns  about  newly  assigned,  weaker  constraints  that overwrite
     previously assigned,  stronger constraints.
     
     *  Molecule-molecule,  molecule-residue,  or  residue-residue distance
     constraints are  now all available.
     
     *  Wildcard selection of all atoms in a molecule with GROUP, MATCH, or
     PLANAR  constraints is now possible.
     
     *  'PDBOUT'  can  now  specify the starting output structure number by
     appending a ':' to  the root filename, followed by the desired number.
     
     *  'PREFIX'  toggles  writing the structure number before or after the
     fileroot when writing  out PDB files.
     
     *  'SPLIT'  writes  each  molecule  to  a separate file with filename 
     <molecule_name><pdbout_name><#>.pdb.    Works   as    expected    with
     'PREFIX:'.
     
     * Modified all boolean commands to take TRUE/FALSE option;  entering a
     command with no  value implies TRUE.
     
     *  Comment lines can be included in DGEOM95 command files;  they begin
     with '!' or '#' and  are echoed to the summary output file.
     
     * Chiral constraints can be reinitialized, clearing all previously set
     chiral constraints (automatic  and user-defined) with the new command:
     CHIRAL INIT.
     
     *  User-defined  random number generator initialization.  'NSEED1' and
     'NSEED2' set the 1st  and 2nd seeds for the random  number  generator,
     and 'NRANDOM' initializes the random number  sequence to the NRANDOMth
     element.
     
     *  'ORIENT'  command  warns  if  less  than  4  atoms  are entered for
     matching.
     
     *  Program COMPARE includes Jarvis-Patrick clustering (Jarvis, R.  A.,
     Patrick, E.  A.   "Clustering Using  a  Similarity  Measure  Based  on
     Shared Near Neighbors", IEEE Trans.  Comp.  1973,  C22, 1025-1034) and
     is  now  completely  self-contained.   COMPARE  reads  a series of PDB
     files,   along   with  (optional)  free-format  input  containing  the
     molecule number, residue number, and names of   atoms  to  match.   It
     calculates  all  pairwise  RMS  least-squares  fit  errors between the
     structures,  generates a distance matrix from the RMS matrix, extracts
     the set of nearest neighbors from the  distance matrix,  and  clusters
     the  nearest neighbor list using the Jarvis-Patrick algorithm to group
     the  structures into 'families'.

     Bug Fixes
     ---------

     * Fixed bug to allow read/write of 4-character residue names.
     
     * Fixed bug which forced the end of a constraints group after reading
     a comment card or blank line.
     
     * Fixed  bug  in  the message warning of more than 4 bonds to a given
     atom.
     
     * Fixed  bug  involving  read/write of the metric matrix to a scratch
     file.
     
     * Fixed  bug  where  automatic  chiral  constraint  generation  could
     overflow the format  statement  in  an   internally  generated  chiral
     command.  
     
     * Chiral  quartets  within  RIGID  groups  are  now  only  set if the
     abs(chiral volume) < threshold, where  threshold ~ max  volume  for  a
     chiral carbon.  Previously, very large volumes between atoms far apart
     in a  structure could lead to severe convergence problems.
     
     * Fixed bug in eigenvalue routine for two-dimensional structures.
     
     * Fixed  bug  in torsion picking routine where upper and lower bounds
     are nearly equal.
     
     * Fixed bug in routine to find aromatic rings.
     
     * Fixed  sulfate/phosphate  bug where planar constraint is mistakenly
     assigned to these groups.