X-PLOR(online) 3.843 available

Axel T. Brunger brunger at LAPLACE.CSB.YALE.EDU
Tue Sep 24 00:59:21 EST 1996


Announcing:        X-PLOR(online)
---------------------------------
New version: 3.843        9/23/96
---------------------------------
Copyright 1996 by Yale University
---------------------------------
---------------------------------


Internet access to X-PLOR(online) version 3.843 is now available 
for non-profit (academic) users holding a license for X-PLOR version 3.1 
from Yale University, free of charge.  

This version is only available via the Internet.

Access instructions are available in our home page http://xplor.csb.yale.edu.
The procedure is identical to that of version 3.840.

IT IS IMPORTANT THAT YOU DOWNLOAD AND INSTALL ALL FILES IN THE
xploron3843_main.tar FILE (SOURCE, XTALMACRO, TOPPAR, XTALLIB, NMRLIB, 
TUTORIAL, DATACONVERSION). DO NOT MIX FILES FROM DIFFERENT VERSIONS.

Features of X-PLOR(online), version 3.843
-----------------------------------------

Summary:

X-ray crystallography:

1. Major update of all X-ray crystallographic tutorial files using new syntax.
2. torsion angle molecular dynamics for crystallographic refinement.
3. probabilistic MAD phasing.
4. sigmaa-weighting for electron density maps with optional cross-validation.
5. difference, anomalous difference, and <n>Fo-<m>Fc electron density maps.
7. Cross-validated coordinate error estimates by Luzzati and Sigmaa method.
8. Script files for molecular replacement with multiple molecules 
9. Automated water picking procedure
10. New bulk solvent refinement procedure
11. Example for resolution-dependent weigthing scheme for refinement
12. Direct rotation function.
13. Phased translation function. 
14. scalepack/denzo -> X-PLOR(online) conversion program
15. X-PLOR(online) -> PDB deposition script (for crystal structures)

Solution NNR spectroscopy:

1. J-coupling restraints
2. proton chemical shift restraints
3. carbon chemical shift restraints


General Remarks
---------------

1. For several months, new parameter and topology files for
   DNA and RNA (dna-rna.top and dna-rna.param) have been available 
   (developed by Prof. Helen Berman and co-workers).  
   These parameters are much improved compared to the older DNA parameters
   of X-PLOR 3.1.  The new parameters can be used in conjunction with 
   the Engh and Huber parameters for proteins (parhcsdx.pro and parhcsdx.pro).  

   DNA and RNA molecules may require some additional restraints.  
   The arestraints.inp  and brestraints.inp in tutorial/generate/
   provide examples how to use these additional restraints.  

2. Electrostatic energy terms have been removed from all crystallographic
   refinement protocols in order to reduce possible bias.   Removal of 
   hydrogens is optional.

3. Unsupported machine versions are now available for DEC alpha VMS and 
   IBM AIX. 


Release Notes for X-PLOR(online), version 3.843
-----------------------------------------------
1. The statement REFL INDEX FOBS will now read negative phases properly.

2. R-Cullis is now included in phasing macros.

3. Separate statistical summaries are generated for centric, acentric,
   and all reflections for phasing power, fom, R-Cullis, R-Kraut, lack
   of closure in phasing macros. 
   
4. The default for XREFin ASELEction has been changed.  It is now equivalent to 
   ASELE=( attribute scatter_fdp > 0.1 ), i.e., for all atoms with 
   f'' > 0.1 the imaginary part of the form factor will be included 
   in the structure factor calculation if ANOMALOUS is set to TRUE.

   Note that the computation of atoms with f'' included uses the
   direct summation, i.e., it is very slow.  The scattering tables
   have f'' components for all atoms (including carbon, nitrogen, etc)
   although f'' is very small for the latter atoms.  Thus, by introducing
   the threshold of 0.1 only those atoms with significant f'' are included
   in the anomalous structure factor calculation.  
  
5. There is a new X-PLOR(online) directory: /dataconversion/  This
   directory contains programs and script files for communication 
   with other programs and the Brookhaven Data Bank. 
  
6. Scalepack-> X-PLOR(online):
   sclpckxplor.f   ! scalepack to X-PLOR(online) conversion program is now
   in directory: /dataconversion/denzo_scalepack/.  Note that this
   program treats anomalous as well as non-anomalous data. 

7. PDB crystal structure submission: 
   in dataconversion/pdb_xtal_submission/xtal_submit.inp
   This file provides most of the information needed for
   PDB submission when X-PLOR(online) is used for crystallographic 
   refinement. However, some additional information may have to be 
   provided by the user and checking of the resulting deposition
   file is advised.     
   
8. Difference map examples in /tutorial/mad directory: experimental map, 
   dispersive difference map and anomalous difference map with 
   several cutoff and selection criteria. 

9. Updated tutorial files using new X-PLOR(online) syntax, libraries, 
   cross-validation for X-ray refinement, molecular replacement, 
   and electron density map calculations. 

10. Cross-validated Luzzati coordinate error estimate 
    (/tutorial/xtal_analysis/luzzati.inp).

11. Cross-validated sigmaa coordinate error estimate 
    (/tutorial/xtal_analysis/sigmaa.inp).

12. New Wilson plot and quasi-absolute scaling procedure
    in /tutorial/xtal_analysis/wilson.inp.

13. A Euclidean normalizer library has been created. 
    The translation search example files in /tutorial/xtalmr/ 
    files have been updated to automatically define the asymmetric 
    unit of the translation function using this library. 

14. Electrostatic energy terms have been removed from all crystallographic
    refinement protocols.  

15. Updated fo-fo, nfo-mfc, sigmaa-weighted, annealed omit
    maps in /tutorial/xtal_maps/.
    
16. Cross-validation of sigmaa-weighting for electron density maps. 

17. All 1-D plot files produced by X_PLOR(online) consist of 
    lists of numbers that can be cut and pasted into popular 
    spreadsheet programs.  MATHEMATICA example files are also provided.  

18. New automated water-picking protocol in /xtal_waterpick/waterpick.inp.

19. New automated bulk solvent model parameter refinement
    (/tutorial/xtalrefine/setup_bulksol.inp).
    
20. Example for resolution-dependent weighting for crystallographic
    refinement (/tutorial/xtalrefine/resolution_dependent.inp).
    
21. NMR proton and carbon chemical shift restraints
    (/tutorial/nmr_shift_coup/mini_shift_coup.inp) see 0read.me file.
    
22. NMR J-coupling restraints
    (/tutorial/nmr_shift_coup/mini_shift_coup.inp) see 0read.me file. 
    
23. Degenerate proton restraints
    (/tutorial/nmr_shift_coup/mini_shift_coup_degen.inp) see 0read.me file.
    
24. One-bond 1JCaHa J-coupling restraints
    (/tutorial/nmr_shift_coup/mini_shift_coup_onebond.inp).
    
25. There are unsupported machine versions available for 
    DEC alpha VMS in machine/unsupported/alpha-vms and 
    IBM AIX in machine/unsupported/ibmaix



Axel T. Brunger




-- 
=======================================================================
| Axel T. Brunger          Dept. Molecular Biophysics and Biochemistry|
| Professor/Investigator   Bass Center, 266 Whitney Avenue            |
| Office: 203-432-6143     Howard Hughes Medical Institute/Yale Univ. |
| FAX:    203-432-6946     New Haven, CT 06520, USA.                  |
| http://xplor.csb.yale.edu/~brunger                                  |
| mailto://brunger@laplace.csb.yale.edu                               |
=======================================================================



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