Announcing: X-PLOR(online)
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New pre-release version: 3.851 10/20/96
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Copyright 1996 by Yale University
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Internet access to X-PLOR(online) pre-release version 3.851 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
xploron3851_main.tar FILE (SOURCE, XTALMACRO, TOPPAR, XTALLIB, NMRLIB,
TUTORIAL, DATACONVERSION). DO NOT MIX FILES FROM DIFFERENT VERSIONS.
Important new features:
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1. Modified parameter files for protein and DNA/RNA using
repulsive non-bonded parameters similar to PROLSQ
(for proteins and water: protein_rep.param and for DNA/RNA:
dna-rna_rep.param). Please use with caution since only
limited testing was performed. Any feedback would
be appreciated.
2. Example for extending the test set from a diffraction data set into
another, e.g. higher-resolution data set
(/tutorial/xtal_free_r/extend_free_r.inp)
Release Notes for X-PLOR(online), version 3.851
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1. Included maximum shift option in heavy atom refinement:
qmaxshift, bmaxshift, fpmaxshift, fdpmaxshift
2. Updated all crystallographic refinement files:
(a) option for fixing atoms
(b) atoms excluded from energy and struc. calc are now fixed
(c) masses are restricted to 40amu in all annealing jobs
(d) NCS restrains and constraints
3. Logical variables and other bug fixes in VMS command files for
alpha-OSF.
4. Introduced new statement FILEEXIST <filename> END. Returns logical
symbol $RESULT. Is TRUE if file exist. Is FALSE otherwise.
5. Fixed bug with backslash operator:
display $CPU \
$CPU[F6,2],$CPU
now works properly.
6. Introduced multiple refinement loop in slowcool examples
(tutorial/xtalrefine).
7. Increased memory statement to 2000000 in all crystallographic
refinement
examples.
8. Using quartic repulsive potential for all crystallographic
refinements.
9. Using fast nonbonded calculation for all crystallographic
refinements.
10. Fixed problem with cross-validated sigmaa fom calculation.
11. Phase restraints parameter wp included in all crystallographic
refinement
files.
12. Extend-free-R example (lower resolution to higher resolution).
in /tutorial/xtal_free_r/extend_free_r.inp.
13. Modified and improved parameter files for proteins
(protein_rep.param)
and DNA/RNA (dna-rna_rep.param). Both files are to be used in
conjunction
with tophcsdx.pro and dna-rna.top. These files contain a repulsive,
quartic
nonbonded function with parameters identical to PROLSQ. The
geometric
parameters are taken from the Engh and Huber protein force field
(parhcsdx.pro)
and the Berman DNA/RNA force field (dna-rna.param). The
protein_rep.param
file also contains water parameters. For the protein parameters,
small
dihedral angle energy constants were set to zero. All other
dihedral
and improper energy constants were set to uniform values. The dna
improper and
dihedral angle energy constants were not modified.
14. Included explicit option for changing targets in crystallographic
refinement files.
15. Fixed bug in pdbsubmission macro: ncs operators were read after
R computation in 3.843 (for strict NCS). The problem occured
when the number of ncs ops > 9.
16. Modified topology and param files for the 5PHO patch for
5'-phosphorylated DNA: dna-rna.top and dna-rna.param.
17. WRITE REFL : by default, the statement now writes all objects
that have been declared and that deviate from default values.
18. NREF: if previous NREF smaller than the new value then
reciprocal-space objects are now extended (were deleted
in previous versions).
19. Changed default resolution lower limit to 8.0 A in all
refinement example files.
20. Updated sgi ulogin.com file.
--
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| 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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