NOESHOW(1)
NAME
- noeshow - show AMBER INTERFACE format NMR-derived
constraints
mardishow - show MARDIGRAS format NMR-derived constraints
SUPPORT PROGRAMS
- sander2amber - convert AMBER SANDER namelist-style distance
- constraints to AMBER INTERFACE format
- xplor2amber - convert X-PLOR distance constraints to AMBER
- INTERFACE format
- xplor2tors - convert X-PLOR torsion angle information to
- AMBER style
- diana2amber - convert DIANA distance constraints to AMBER
- INTERFACE format
MIDAS COMMAND SYNTAX
- Command: noeshow [ options ] constraint_file [ torsion_file
]
or
Command: mardishow [ options ] constraint_file
SHELL COMMAND SYNTAX
- sander2amber pdb_file sander_input_constraints >
reformatted_constraints
diana2amber [ -v viol_add ] pdb_file diana_low_bounds
diana_high_bounds > reformatted_constraints
xplor2amber [ -c chain_ID ] [ -v viol_add ] pdb_file
xplor_constraints > reformatted_constraints
xplor2tors [ options ] xplor_torsion_output >
reformatted_torsion_file
DESCRIPTION
- Noeshow and mardishow are programs for displaying NMR-
derived constraints on model structures in MIDAS. Noeshow
can display distance constraints in AMBER INTERFACE format
and, via format conversion programs, constraints in X-PLOR,
DIANA, MARDIGRAS (output), or AMBER SANDER (namelist)
formats. Mardishow can display constraints in MARDIGRAS
input or output formats. Noeshow's functionality is
generally a superset of that provided with mardishow, and
mardishow is provided principally for its ability to display
MARDIGRAS input format constraints. If a conversion program
for MARDIGRAS input format is developed, mardishow may be
withdrawn.
- Noeshow can also show torsion angle constraints if given the
restraint analysis output from the SANDER AMBER module. The
conversion program xplor2tors can be used to convert X-PLOR
torsion angle information to a form usable by noeshow.
- Finally, noeshow can be used to indicate all hydrogens
within a given cutoff distance of one or more designated
hydrogens. This capability can be used with or without an
accompanying set of distance constraints.
USAGE
Distance constraint preparation
- If your distance constraints are in AMBER INTERFACE format,
they need no further preparation to be used by noeshow. If
you have constraints in MARDIGRAS input format, they are
ready for use in mardishow (see the ``Mardishow'' section,
below). Constraints in other formats will need to be
converted. If you are not certain what format your
constraints are in, examples of each are provided in the
``Constraint formats'' section below.
- Constraints in AMBER INTERFACE format have an ``energy
well'' for each constraint. There are two upper-bound
values and two lower-bound values. The lower of the two
upper-bound values is where (if the distance exceeds the
bound) an energy penalty begins to be applied (in the AMBER
simulation) and the higher upper-bound value is where the
penalty reaches a maximum. The lower bounds are similar,
but apply to short distances. Some constraint formats (e.g.
X-PLOR) describe only one upper and one lower bound. How
this is mapped to the AMBER INTERFACE-type constraint style
depends on the conversion procedure. The conversion
procedure for the various formats are:
- X-PLOR
- Running the xplor2amber conversion script (as shown in
the SHELL COMMAND SYNTAX section, above) will produce a
file of equivalent constraints in AMBER INTERFACE
format. The bounds given in the X-PLOR constraint file
are taken as describing the ``floor'' of the energy
well required for the AMBER INTERFACE format
description, i.e. the distances where an energy penalty
would begin to be applied. The distances where the
energy penalty reaches a maximum is taken to be 0.5
angstroms beyond the given bounds on either side. The
default value of 0.5 can be changed by giving the -v
option flag to xplor2amber, followed by the desired
distance. As described later, the bounds of the energy
well determine whether the constraint will be shown as
satisfied or violated (see the ``Basic usage''
section).
- Xplor2amber will normally interpret segids in the X-
PLOR constraint file as chain IDs in the converted
file. The ``-c chain_ID'' option to xplor2amber will
cause it to give all atoms the specified chain ID.
Note that specifying chain_ID as " " (a quoted space)
will give the atoms no chain ID, even if segids are
present in the X-PLOR constraint file.
- DIANA
- DIANA format constraints are handled in almost the same
manner as the just-described X-PLOR format constraints.
The only differences are that the conversion script is
diana2amber instead of xplor2amber, and that instead of
specifying a single bounds file on the command line,
separate lower- and upper-bounds files (in that order)
are specified. Also, there is no -c option for
diana2amber.
- AMBER SANDER (namelist)
- Running the sander2amber conversion script (as shown in
the SHELL COMMAND SYNTAX section, above) will produce a
file of equivalent constraints in AMBER INTERFACE
format. Since AMBER SANDER constraints already
describe an energy well, the mapping to an AMBER
INTERFACE energy well description is straightforward.
- MARDIGRAS (output)
- Although mardishow is capable of displaying MARDIGRAS
(output) format constraints without conversion, it may
nonetheless be desirable in certain circumstances to
convert the constraints for use with noeshow in order
to make use of features only present in the latter
program. Such a conversion is a two-step process.
First, the constraints are run through the mardi2amber
program to convert them to AMBER SANDER (namelist)
format. The mardi2sander program is provided with the
MARDIGRAS package, and is documented there. The second
step is to convert the AMBER SANDER format constraints
to AMBER INTERFACE format, as detailed in the paragraph
above.
Torsion angle constraint preparation
- You need not have torsion angle constraint information in
order to use noeshow or mardishow; such information is
optional. In fact, mardishow cannot display torsion angle
constraint information, only noeshow can.
- Noeshow uses the output torsion angle restraint information
from the SANDER AMBER module, rather than the input torsion
angle info. This is because it uses the energy penalty
information provided by AMBER to color the torsion
constraints. A sample of the kind of information it expects
can be found in the ``Constraint formats'' section of this
document.
- Torsion angle information from X-PLOR can be converted for
use with noeshow. Again, this is output information and,
again, an example is provided in the ``Constraint formats''
section. The X-PLOR output information can be converted to
the AMBER format with the xplor2tors program, the procedure
for which is shown in the SHELL COMMAND SYNTAX section,
above. X-PLOR torsion constraints are expressed as a
desired angle and an allowable range about that angle.
Xplor2tors has two options to control the transition from
satisfied (green) to slightly violated (yellow) to badly
violated (red). The ``-a degrees'' option controls how
close to the edge of the range an angle can be before it is
shown as slightly violated (default: 5 degrees). The ``-A
degrees'' option controls how far beyond the edge of the
range an angle can be before it is shown as badly violated
(default: 10 degrees).
Basic usage
- This section will discuss how to use noeshow to display NMR
constraints in MIDAS. Mardishow is used in a very similar
manner, and any differences will be discussed in the
``Mardishow'' section, below.
- Noeshow is run from within MIDAS, so the first step is to
display the model structure (or structures) in MIDAS. Once
you've done that, invoke noeshow as shown in the MIDAS
COMMAND SYNTAX section above. The parts of the command
enclosed in brackets ([]) are optional and can be omitted.
- Noeshow will read the file(s) you specify and generate and
display a graphics object depicting the distance constraints
and torsion angle constraints (if any). For the curious,
graphics objects are discussed in the ``Non-Molecular
Graphics Objects'' section of the MidasPlus manual, though
it is not necessary to read that section to use noeshow
effectively. The graphics object will be opened in the
lowest unused model number.
- Distance constraints will be depicted as lines connecting
the atoms involved in the constraint. If one of the
``atoms'' is actually a pseudo-atom composed of several
atoms, then the constraint will be drawn to the nearest of
the atoms. The distance constraints will be colored
according to how well they are satisfied:
| Color |
Meaning |
| red |
distance exceeds both upper bounds |
| yellow |
distance between the upper bounds |
| green |
distance satisfies constraint |
| cyan |
distance between lower bounds |
| blue |
distance less than both lower bounds |
- Note that by default noeshow does not display the satisfied
constraints (the -a flag causes them to be displayed).
- Torsion angle constraints (if any) will be displayed as
``cages'' surrounding the central bond of the dihedral. The
coloring of the cage is as follows:
| Color |
Meaning (AMBER)Meaning (X-PLOR) |
| red |
energy penalty > 4.0violation > 10 degrees |
| orange |
energy penalty > 1.0violation < 10 degrees |
| yellow |
energy penalty > 0.0satisfied, but within 5 degrees of violated |
| green |
energy penalty = 0.0satisfied and not within 5 degrees of violated |
- Note that X-PLOR torsion coloring can be adjusted with
options to the xplor2tors conversion script.
- By default, noeshow will not display the satisfied torsion
angle constraints. The -A option flag will cause them to be
displayed as well.
Restricting display
- By default, noeshow displays all the violated constraints
present in the constraint file. At times, this may be more
information than is desired. There are several methods of
restricting the displayed constraints to those of interest,
detailed below.
- In the early stages of structure refinement, it may be
desirable to show only the badly violated constraints (if
you are uncertain about all the cross-peak assignments, for
example). Giving noeshow the -v option will restrict the
display to only badly violated constraints (i.e. those
colored red or blue).
- The simplest way to restrict constraint display to specific
areas of the structure is to undisplay the parts of the
structure where you don't want constraints shown. Noeshow
will not show constraints where one or both ends would be on
an undisplayed part of the structure. To get this effect,
you have to undisplay the undesired regions before running
noeshow. You could then redisplay the whole structure after
having generated the constraints of interest. Undisplaying
parts of the structure after running noeshow has no effect
on displayed constraints.
- There is a somewhat more complicated method for restricting
constraint display that offers finer-grain control than the
above method. It involves using the relatively new mark and
makemark commands of MIDAS. You may want to read the
documentation for the above two commands in the MidasPlus
manual if you are unfamiliar with them. These commands
allow you to mark a set of atoms with a name. If you mark a
set of atoms with the name ``noemark1,'' then noeshow will
only show constraints where at least one end involves an
atom in the marked set. If you also mark some atoms with
the name ``noemark2,'' then noeshow will only show
constraints where one end is in the first set and the other
end is in the second set. For example:
- makemark noemark1
- would create the mark name ``noemark1'' for use, and:
- mark noemark1 :12-14
- would mark all atoms in residues 12 through 14 with the name
``noemark1.'' Running noeshow at this point would show only
those constraints that had at least one end in residues 12
to 14.
- Note that running the mark command with the same name a
second time will add to the set of marked atoms, not replace
the set with a new set. To replace, you would have to clear
the mark with ``~mark name'' and then mark with the new set.
Structure Ensembles
- To determine constraint satisfaction across an ensemble of
structures displayed in MIDAS, noeshow uses exponential
averaging (``R to the minus sixth''). The color-coded
results are displayed on the highest-numbered open model.
The same flags used to control pseudo-atom averaging (-D and
-x) also control the ensemble averaging (see Options
section). The -c flag, however, is ignored for ensemble
averaging. If you want simple numerical averaging for the
constraints, use ``-x 1'' instead of -c.
- Normally, noeshow will give equal weight to each member of
an ensemble. It is possible, however, to give the members
unequal weightings. This could be useful, for example, if
the ensemble had been generated by a program such as PARSE
[1], which assigns a probability to each member of the
ensemble. To indicate the weights to noeshow, there must be
a line in each PDB file, as follows:
- USER STRUCTURE WEIGHT weight
- where weight is any non-negative number. Note that there
are two spaces after the USER. Structures lacking a line
such as the above will be given a weight of 1.0 (and
therefore, if no structures have the above line, all will
have equal weight).
Showing possible H-H interactions
- Noeshow has one capability that is designed to be used
primarily without a set of distance constraints: it can
show all hydrogens within a given cutoff distance of one or
more designated hydrogens. The general procedure to do this
is to use the marking mechanisms discussed in the
``Restricting display'' section to designate both the
hydrogens of interest (marked with noemark1) as well as the
neighboring hydrogens that should be considered for the
cutoff (marked with noemark2). Then noeshow would be run
with the ``-h cutoff'' option to specify the cutoff
distance. Noeshow will draw a pink line between each pair
of hydrogens satisfying the cutoff criterion and will show
the corresponding distance at the midway point of the line.
- Since noeshow is implemented as a perl script, it is not
very fast at numerical calculations. It is therefore best
if you limit the marked sets of atoms to the smallest sets
that still have all the atoms of interest. For example,
let's say you have marked one or more hydrogens with
noemark1, and you intend to run noeshow with a cutoff
distance of 5 angstroms. You could simply not mark any
atoms with noemark2, in which case noeshow would have to
calculate the distance from every hydrogen marked with
noemark1 to every other hydrogen in the molecule. It would
speed things up considerably to use noemark2 to mark only
those atoms that could possibly satisfy the cutoff, with a
command such as:
- mark noemark2 /mark=noemark1 za<5.1
- which marks all atoms within 5.1 angstoms of the atoms in
noemark1 with the mark noemark2 (this is one of the more
advanced uses of atom specifiers; you may want to look at
``Referencing Models, Residues, and Atoms'' in the MidasPlus
manual for further information, particularly the section
``Atom Properties'').
- You need not mark one very small set of atoms and one larger
set; you could mark approximately equally sized sets of
atoms as long as the set size isn't too large (perhaps a few
dozen atoms each). For example, if you were working with a
nucleic acid structure and marked all H1*'s with both
noemark1 and noemark2, and then used a cutoff of about 5
angstroms, the resulting helical ``chain'' of H-H lines
would show where the structure had fairly even distances as
well as where there were ``breaks'' in the structure.
- The -h option was designed to be used with no distance
constraint file, and is the only option that allows the
distance constraint file to be omitted from the command
line. Nonetheless, you can specify a distance constraint
file and it will be shown normally. Note that since the
marking mechanism is normally used to restrict constraint
display, any marks used to delimit H-H interactions will
also restrict displayed constraints.
Tips on usage
- Displaying multiple constraint sets
- There are times that it is desirable to display several
different constraint files separately. For example, if
you've divided your constraints into positive
constraints (distances determined from a cross-peak:
the atoms must be at most a certain distance apart) and
negative constraints (distances determined from the
absence of a cross-peak: the atoms must be at least a
certain distance apart), then you might like to show
these sets separately at first and then together. To
do this, you would run noeshow once for each constraint
set you want displayed. Noeshow will open each
successive graphics object in a different model number
(the lowest available at the time). You can then
undisplay specific graphics objects with the
``~objdisplay modelnum'' command. ``objdisplay
modelnum'' will, of course, redisplay them while
``close modelnum'' will dispose of them permanently.
- Showing only torsion restraints
- Showing torsion constraints with no distance
constraints may seem problematic at first, since
noeshow requires an argument specifying a file of
distance constraints. However, this is simple to get
around by specifying a distance constraint file that is
empty. On UNIX systems (such as the SGI) there is a
special system file that is always guaranteed to be
empty: /dev/null. Therefore, invoking noeshow as:
- noeshow [ options ] /dev/null torsion_file
- would display only the torsion constraints in
torsion_file.
Options
- Many default behaviors of noeshow can be modified by
command-line option flags. The options supported by noeshow
are:
- -a
- Show all constraints, including satisfied constraints.
- -A
- Show all torsions, including satisfied torsions.
- -c
- For multi-atom pseudo-atoms, measure constraint to
geometric centers of atoms rather than doing
exponential averaging. See also the -D and -x flags.
- -D
- Don't divide by number of atoms when doing exponential
averaging of pseudo-atoms. See the -x flag for more
info.
- -e lowbound
- Change the lower energy penalty threshold (where
torsion colors change from green to yellow) to
lowbound. Default is 1.0.
- -E hibound
- Change the upper energy penalty threshold (where
torsion colors change from yellow to red) to hibound.
Default is 4.0.
- -f file
- Store violated constraints in a file named file, sorted
by magnitude of violation. See also the -n flag.
- -F
- Don't quit on encountering the first error; continue to
report errors. This is useful when debugging problems
using noeshow, which is discussed in the next section.
- -h cutoff
- Show hydrogen-hydrogen interactions that are no more
than cutoff angstroms apart. See the ``Showing
possible H-H interactions'' section for a description
of this option. If this option is specified, the
constraint file command-line argument can be omitted.
- -l
- Label atoms involved in unsatisfied constraints. For
pseudo-atoms, only the atom that the constraint is
drawn to (the closest) is labeled.
- -L
- Expect LEaP nomenclature for atom names. LEaP is a
module provided with AMBER. If you don't know what
LEaP is, you don't care about this flag!
- -n
- Used in conjunction with the -f flag; show signs as
well as magnitudes of violated constraints.
- -v
- Show only badly violated distance constraints.
- -V
- Show only badly violated torsion constraints.
- -x exponent
- Control the exponent used in exponential averaging of
distances involving pseudo-atoms. Unless given the -c
flag, noeshow does exponentially-weighted averaging of
distances involving pseudo-atoms. If a constraint
involves n atoms on one end and m atoms on its other
end, then the weighted average distance is:
|RR|c->n-c->m|exponent|____1
|n_m__________________|exponent
| n.m |
| |
where ci is the coordinate position of the ith atom.
The default exponent is -6. Use of the -D flag
prevents the division by n.m.
Errors
- Noeshow displays error messages in the MIDAS reply area.
Errors typically occur when there are problems matching atom
names in the constraint file with those in the PDB file.
Frequently in such cases many error messages are generated.
In the Iris GL version of MIDAS, only the last few of these
can be seen in the reply area.
- If it is necessary to see all the error messages at once,
this can be done by running noeshow outside of MIDAS . The
first step is to get a PDB file from MIDAS to use as input
to noeshow. In MIDAS, issue the command:
- pdbrun cat > inputfile
- This will save an annotated PDB file describing the current
MIDAS display into a file called inputfile. Next, from a
shell window, run:
- /usr/local/midas/lib/midas/noeshow options_used_in_Midas < inputfile
- The output from the above command will be a series of MIDAS
commands. The output commands that start with echo are the
ones that would display messages in the MIDAS reply area.
Note that one of the output commands starts with !rm. This
is to get MIDAS to remove a temporary file that noeshow
produces. You may wish to remove this temporary file
yourself by typing in the output ``rm'' command to the shell
window, less the leading ``!.''
Mardishow
- Mardishow is used to display constraints that are in
MARDIGRAS input format and can be used to display
constraints in MARDIGRAS output format, though noeshow can
be used to display MARDIGRAS output also, as outlined in the
``Distance constraint preparation'' section, above. This
section will outline the salient differences between using
noeshow and mardishow.
- Mardishow displays constraints in the two MARDIGRAS formats
directly, i.e. the constraints do not need to be converted
to an intermediate format, unlike the procedure for noeshow.
- Since neither MARDIGRAS input nor MARDIGRAS output format
constraints have an ``energy well'' associated with them,
displayed constraint violations are color-coded differently
than in noeshow. When showing MARDIGRAS output format
constraints, mardishow constructs a ``fake energy well'' by
using the given upper and lower bounds to define the
``floor'' of the energy well. The ``edges'' of the well are
placed 0.5 angstroms beyond the given bounds (this margin
can be changed with the -d option). Coloring is then as in
noeshow. For MARDIGRAS input format constraints, the
coloring scheme is simple: if the distance is less than 5
angstroms then the constraint is colored green, if between 5
and 6 angstroms yellow, and greater than 6 angstroms red.
- Mardishow does not support restricting constraint display,
either through the ``marking'' mechanism of noeshow or by
undisplaying parts of the molecule. Bad things will happen
if you try.
- Pseudo-atom constraints are measured to the heavy atom
connected to the hydrogens, rather than involving any kind
of averaging.
- Mardishow is designed to work with a single model structure
rather than an ensemble. The only way to use mardishow in
conjunction with an ensemble is to display one structure of
the ensemble at a time.
- Mardishow supports a subset of the flags of noeshow, namely:
-a, -f, -F, -l, and -n. In addition, it has the following
flags:
- -d amount
- When displaying MARDIGRAS output format constraints,
make the outside bounds of the ``energy well'' amount
angstroms from the inner bounds (which are given in the
constraint file).
- -s
- Enable ``stereospecific'' constraints. If a constraint
names a hydrogen involved in a rotamer and this option
is given, then the constraint will be measured and
drawn to that hydrogen. Otherwise, the constraint will
go to the connected heavy atom.
FORMAT EXAMPLES
AMBER INTERFACE format
- restraint/ at1=2:HA /at2=2:HN \
- /r1=2.664 /r2=3.164 /r3=3.252 /r4=3.752 /k2=1.000 /k3=1.000 \
and/or
restraint / at1=1:H23 /at2 =1:H25 \
/r1 = 0.0/r2=1.8000/r3=2.5980/r4=4.5980/k2=10.0/k3=10.0 \
/grpat1 =1:H23,1:H24
and/or
restraint / at1=275 /at2 =290 \
/r1 = 0.0/r2=1.8000/r3=2.5980/r4=4.5980/k2=10.0/k3=10.0 \
/grpat1 =275, 276
AMBER SANDER namelist format
- &rst
- iat = 37, 35, iresid = 1, atnam(1)='H8 ',atnam(2)='H2''2',
r1 = 0.000, r2 = 2.895, r3 = 2.945, r4 = 4.945,
rk2 =10.000, rk3 =10.000, &end
and/or
&rst iat = 108, -1,
igr2 = 143,144,145,0,
r1 = 0.000, r2 = 3.315, r3 = 3.395, r4 = 5.395,
rk2 =10.000, rk3 =10.000, &end
X-PLOR distance constraint format
assign (resid 6 and name HB )(resid 7 and name HN ) 4.0 2.2 1.0
assign (resid 34 and name HB# )(resid 39 and name HN ) 4.0 3.7 2.5 !
assign (resid 37 and name HB1 )(resid 39 and name HN ) 4.0 2.2 1.0
assign (resid 23 and name HB# )(resid 26 and name HB# ) 4.0 5.2 4.0 ! !#
assign (resid 22 and name HB2 )(resid 24 and name HN ) 4.0 2.2 1.0
assign (resid 20 and name HB# )(resid 22 and name HN ) 3.0 2.7 2.0 !
DIANA low and high bound constraint format
| 14 TYR HN |
10 VAL O |
2.00 1.00E+00 # H-Bond |
| 13 ARG HN |
14 TYR HN |
2.90 1.00E+00 # N(i)-N(i+1) |
| 11 VAL HA |
14 TYR HN |
5.00 1.00E+00 # ha(i)-hn(i+3) |
| 14 TYR HA |
17 ALA QB |
3.80 1.00E+00 # ha(i)-hb(i+3) |
| 14 TYR HA |
29 LEU QD1 |
3.80 1.00E+00 # helix1-helix2 |
| 14 TYR QR |
15 VAL QG2 |
7.80 1.00E+00 # sequential |
| 18 LEU QD1 |
14 TYR QR |
7.80 1.00E+00 # |
| 24 ASP O |
28 ALA HN |
1.80 1.00E+00 # hbond |
| 25 GLY HA1 |
28 ALA HN |
5.00 1.00E+00 # aH(i)-HN(i+3) |
AMBER torsion information format
- ------------------------------------------------------------------------------
- Final Restraint Analysis for coords: min8.rst
Restraints, deviations, and energy contributions: pencut = .00
------------------------------------------------------------------------------
First atom Last atom curr. value target deviation penalty
------------------------------------------------------------------------------
.
.
.
CA CYX 16 -- CB CYX 16: 212.978 210.000 2.978 .863
CA SER 17 -- CB SER 17: 29.656 30.000 .344 .011
N SER 19 -- CA SER 19: -158.920 -60.000 .000 .000
CA SER 19 -- CB SER 19: 41.668 90.000 .000 .000
CA CYX 20 -- CB CYX 20: 188.804 210.000 .000 .000
N ARG 23 -- CA ARG 23: -59.704 -60.000 .296 .009
X-PLOR torsion information format
---------------------------------------------------
Number of dihedral angle constraints= 130
overall scale = 200.0000
========================================
3 GLN C
4 LYS N
4 LYS CA
4 LYS C
Dihedral= -126.639 Energy= 0.000 C= 1.000 Equil= -157.500 Delta= -0.86
1
Range= 30.000 Exponent= 2
========================================
4 LYS C
5 THR N
5 THR CA
5 THR C
Dihedral= -111.196 Energy= 0.000 C= 1.000 Equil= -120.000 Delta= 0.00
0
Range= 30.000 Exponent= 2
========================================
FEEDBACK
- Feel free to mail suggestions or questions to
pett@cgl.ucsf.edu .
NOTE
- Noeshow and mardishow are perl scripts and, as such, require
a perl command interpreter in order to work. Most systems
already have a perl interpreter installed. If yours does
not, one is provided in the MidasPlus distribution. Consult
the MidasPlus Installation Guide for further details.
REFERENCES
- [1] Ulyanov NB; Schmitz U; Kumar A; James TL.
- Probability assessment of conformational ensembles: sugar
repuckering in a DNA duplex in solution.
Biophysical Journal, 1995 Jan, 68(1):13-24.
AUTHOR
- Eric Pettersen
- UCSF Computer Graphics Laboratory
ACKNOWLEDGEMENTS
- Noeshow and mardishow could not have been written without
the assistance and encouragement of Dr. Shauna Farr-Jones.
- Xplor2amber was written with the assistance of Dr. Bryan
Finn and Dr. David Schweisguth, and xplor2tors with the
assistance of Dr. Brian Jones. Diana2amber was written with
the assistance of Dr. Michael Zawrotny.