Uppsala Software News @ 970808
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           http://xray.bmc.uu.se/~gerard/manuals
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* LSQMAN Version 6.1
********
I have implemented a set of (simple) commands to produce VRML
files of (aligned) molecules, so you can inspect "on-the-fly"
how your superpositioned structures look, without having to
save the molecules to PDB files, fire up a graphics program,
etc.  For details, see the manual.
  New commands to generate plots of the circular variance of
the main-chain (phi, psi; command VM) and side-chain dihedrals
(chi1, chi2; command VS) for multiple models (NCS or NMR).
The circular variance is a number between 0 and 1, with low
values indicating a high degree of similarity of corresponding
dihedrals in the various models.  See the manual for details.
  The default value for the SEquential_hits constraint parameter
is now ON instead of OFf (affects the IMprove and BRute_force
commands; can be toggled with the SEt SEq command).
  The convergence detection of the IMprove option has been
changed so that the process now finishes as soon as no
further improvement is achieved (previously, it only stopped
if the fit deteriorated from one cycle to the next).  This
slightly speeds up the BRute_force command.
  The IMprove command has been further improved by the addition
of a frameshift correction (which is ON by default and can be
toggled with the SEt SHift command).  For all fragments matched
between two molecules/chains, the program checks if changing
the alignment by one residue in either direction gives a lower
RMSD; if this is the case the shift is applied and the program
checks again.  This is particularly useful when you use a very
liberal matching distance cut-off (e.g., 6 A).  For a typical
comparison using a 6 A cut-off (1AYH versus 1CEL), the old
algorithm gives 169 matches with an RMSD of 2.98 A, and the
new one gives 170 matches with an RMSD of 2.74 A (with 8 of the
17 fragments found shifted by +1 or -1 residue).  This issue
is also important if you want to investigate/publish structure-
based sequence alignments !


* MAMA Version 5.0.1
******
Like LSQMAN, this program now contains a simple VRML interface.
You can display masks (as dot surfaces) and molecules (as
CA [or some other atom type] traces).  Very handy to quickly
inspect a new or improved mask, to compare a mask with an
older one, etc.  See the manual for details.


* XVRML Version 0.2
*******
A simple little jiffy program to generate VRML files from PDB
files.  Options include wire, ball-and-stick and CPK models.
This is a new program (part of X-UTIL; no ESV version !).  There
is a minimal write-up with instructions for use.


* MOLEMAN2 Version 2.1.2
**********
If XVRML is too simplistic/inflexible, use MOLEMAN2 which now also
includes a VRML interface.  Clever combinations of the SElect and VRml
commands can be used to generate very cute pictures.  See the
manual for more details.
  There is a new macro in OMAC, called "make_vrml.momac" to quickly
and automatically create an interesting VRML "world" from any PDB
file.
  The SElect NUmeric command can now also be used to make selections
based on chemical element number, covalent bond radius, and atomic
mass.  In addition, it can now handle BUtnot in addition to ANd and OR.
  New SElection commands: SElect BY_residue, SElect DIstance, SElect
BUtnot.  See the manual for details.
  Fixed a bug in the calculation of the radius-of-gyration (STats
command; thanks to Sherry Mowbray).
  Atom names in the library file ("moleman2.lib") may now contain "?"
wildcards.  E.g., some people call their water oxygen " O  ", others
call it " O1 ", " OHH", etc.; using " O??" in the library captures all
of these (similarly for metal ions).  There is a new version of the
library file "moleman2.lib", which contains these wildcards for a number
of residue types, and which also has improved entries for nucleic acids.


* O2D Version 4.5
*****
New VRML command to convert 2D plot files into VRML.  Don't
know if this is useful ;-)  Not available for ESV and SGIs
running pre-5.3 versions of Irix.


* DEJAVU Version 5.2
********
If you request that DEJAVU generates an input file for LSQMAN,
this file will now also contain instructions for LSQMAN to
write each aligned hit to a PDB file (this option can be
switched off with the PArameter command).  This makes DEJAVU
more useful for people who don't have access to O.


* HETZE Version 0.4
*******
Changed the automatic plane detection a trifle.


* OMAC Public Domain Directory
******
- the following MAMA macros now create a VRML file of the mask
  they produce: cavities.mamac, pdb_mask.mamac, bones_mask.mamac
- the LSQMAN macro ana_ncs.lsqmac now also produces plots of
  the circular variance of phi, psi, chi1, and chi2
- the MOLEMAN2 macro amore_solution.momac now writes the search
  model and the solution to a VRML file
- new MOLEMAN2 macro make_vrml.momac, to generate a VRML world
  from a PDB file


--cd

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