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Technical Differences
Between X-PLOR 98.0/98.1 and CNX 2000

X-Ray: New Features

  • Image-seeking Minimum Function
  • Symmetry Minimum Function
  • Peak search
  • Rotation search clustering
  • Compact fast translation search
  • Multiple map storage/retrieval (maps)
  • Density interpolation
  • Map/mask IO

 

X-Ray General: Changes in CNX include:

  • XRAY statement replaces XREFIN
  • Many changes to XRAY statement options
  • Features moved from code to task files
  • More flexibility

 

NMR: New Features and Enhancements in CNX include:

  • Diffusion anisotropy restraints (DANI)
  • Susceptibility anisotropy restr. (SANI)
  • Ensemble averaged J-coupling restr.
  • Ensemble averaged dipole-dipole cross correlated relaxation rate constraints.

 

New Molecular Dynamics Algorithm

  • Cartesian MD using Verlet leapfrog algorithm
  • Velocity rescaling
  • Temperature coupling
  • X-PLOR dynamics added to CNX.

 

Four Available Minimizers

  • Powell
  • Adopted Basis Newton Raphson (new in X-PLOR 98.1)
  • Limited BFGS minimizer (new)
  • Rigid

 

Atomic Data Model

CNX has an extended atomic data model. In CNX, atoms are uniquely identified by 6 labels:

  • Atom name
  • Residue name
  • Residue id (includes insertion character)
  • Segment id
  • Chain id (new)
  • Alternate location (new)

Other new atom labels/parameters in CNX include:

  • Entity id (mmCIF)
  • Atomic symbols
  • Anisotropic displacement parameters (U matrix)
  • PDB record name
  • TER markers (limited)

 

Parser: Parameters

CNX supports symbols ($name) and parameters (&name)

  • Parameters are stored streams
  • Only defined/changed using a DEFINE() statement
  • Used to store selections, commands, symbols, objects, etc. and passed to modules

 

Parser: Scope

In X-PLOR all symbols were global; in CNX, symbols and parameters have scope

  • New scoping range invoked by @ and @@ unless following an "inline" statement
  • All symbols passed by value (changes made to symbols in module or macro are lost)
  • Parameters should be explicitly passed to new scope

Other new parser commands include:

  • define() - used to define/change parameters
  • inline @ - don’t change scope when switching streams
  • literal - same as display but no $, & substitution
  • FOR <symbol> IN ALTSET <basic-loop> - loops over unique values of ALT
  • buffer - store remarks in named buffers
  • procedure - named subroutines

 

File Input/Output Formats

CNX supports two structure formats: PSF and MTF:

  • Extended PSF Format
    • Backwards compatible with X-PLOR 98.1
    • Added 1-character chain and alt identifiers
  • MTF Format
    • mmCIF extension (true STAR file parser)
    • CNS compatible reader
    • Borrows ext. names from atom_site category

PDB: Full input/output supported for:

  • ATOM/TER/HETATM/ANISOU
  • MODEL/ENDMDL
  • (SSBOND, CRYST1)

mmCIF: Support PDB equivalent fields in categories

  • ATOM_SITE (plus entity_id)
  • ATOM_SITE_ANISOTROP
  • ENTITY_POLY_SEQ
  • CELL

 

Reflection Input/Output Formats

CNX supports the following formats

  • X-PLOR/CNX format (IO)
  • mmCIF (IO)
  • Various third party ASCII formats (input only)

 

Structure Builder

The segment statement has been extended

  • Ability to read unedited PDB files
  • Ability to build multiple structure from a single coordinate file
  • Inclusion of extensive naming options (entity, chain, resid, segid) supplement the molecule, sequence and coordinate builders
  • Ability to build SS bonds from SSBOND records

 

Automatic Discrete Disorder in CNX

  • Alternate locations defined by
  • Reading structure file
  • Reading coordinate file
  • DUPLicate ALT command

 

Automatically ...

  • Builds topology for discrete disorder
  • Identifies polar hydrogen atoms to promote to discrete disorder
  • Defines multiple asymmetric interacting groups modeling discrete disorder

 

Asymmetric Interactions

IGROup Interactions

  • New statement AWEIght used to define asymmetric force weights
  • Default set for all atoms interacting within the model for discrete disorder

 

Miscellaneous

Other differences between CNX and X-PLOR:

  • Force field naming convention consistent with PDB
  • Use OpenMP for shared-memory parallelism
  • Module getcoords takes care of "END" added when reading coordinate files
  • hbuild removed from CNX