Noeshow is a MidasPlus extension program that assists in the visualization of NMR-related data. Noeshow can show distance constraint and torsion angle satisfaction on a model structure or on an ensemble of model structures. Noeshow can use constraints in the following formats:
* AMBER INTERFACE
* AMBER SANDER
* DIANA
* MARDIGRAS
* X-PLOR
Noeshow can also show all hydrogen hydrogen distances within a certain cutoff distance of specified hydrogens.
This document is a walkthrough of the basic functionality of noeshow; it is not a complete reference guide and omits mention of some less-commonly used aspects of noeshow. However, the noeshow manual page is appended to the end of this document and the manual page covers all features of noeshow in complete detail, though in a somewhat less readable style. If you will be using noeshow for "real" work, you should read the manual page after completing these exercises.
This exercise assumes basic familiarity with Midas from other exercises.*
This exercise outlines the procedure for converting and displaying distance con straints. The steps outlined are:
* Distance constraint conversion
* Distance constraint display
* Saving constraint satisfaction data
The "native" format for noeshow is AMBER INTERFACE format. Other con straint formats are converted to this format via conversion scripts. This exer cise shows the conversion (and use) of X-PLOR constraints. Converting other formats is very similar (typically just a different conversion script name). Con sult the noeshow manual page for the exact conversion procedure for your preferred constraint format.
FIrst, you need to make copies of the exercise data files. A script has
been prepared to do this for you. To execute the script, type:
/usr/local/midas/demos/tutorial/noe/copy
This will create a subdirectory of your home directory named noe.ex with
the exercise files in it. If you aren't already in your home directory,
get there with:
cd
Then go to the noe.ex subdirectory with:
cd noe.ex
The first thing is to convert the X-PLOR distance constraints to noeshow's
"native" format. The X-PLOR constraints are in the file noe.xplor. The conversion
script also needs to have access to the PDB file of the model structure
in order to check that it can match the constraints to atoms in the model.
The PDB model structure is in model.pdb. Therefore, the command to convert
the constraints and have them placed in a file named noe.cnst is:
xplor2amber model.pdb noe.xplor > noe.cnst
As mentioned above, the commands for converting other constraint formats
are typically extremely similar. For example, the command to convert AMBER
SANDER style constraints would be:*
sander2amber model.pdb noe.sander > noe.cnst
Consult the noeshow manual page for further details.
Starting Midas
Start Midas with the model structure displayed with:*
midas model.pdb*
Position the model structure however you prefer.
Showing violated constraints
To show the violated constraints on the model structure in Midas, type:
Command: noeshow noe.cnst
You will see some colored lines repre senting constraints between atoms
in the structure. The yellow lines represent distances that are slightly
too long to satisfy their constraints, whereas the cyan lines represent
distances that are slightly too short. The model structure is fairly good.
For a bad structure you would also see red lines (distance much too long)
and dark blue lines (distance much too short).*
Violation criteria
What determines "slightly" too long versus "much" too long? Noeshow's "native" constraint format ( i.e. AMBER INTERFACE format) uses an "energy
well" description of constraint satisfaction. There is a distance range
where the constraint is completely satisfied (zero energy penalty). Outside
of this range, there is a range where an energy penalty is increasingly
heavily applied. Finally, outside this second range, a maximum energy penalty
is applied. Distances in this last range are "much" too short/long whereas
distances in the intermediate range are "slightly" too short/long.
X-PLOR format doesn't have an "energy well" description but instead has
simple upper and lower bounds. To generate an energy well, the xplor2amber
con version script uses the given bounds as the ends of the "zero energy
penalty" and puts the "maximum energy penalty" area 0.5 angstoms beyond.
This can be controlled with a command line option to xplor2amber, as described in the noeshow manual page.
Saving violations to a file
You may wish to save the constraint violation information to a file for
later reference. If you run noeshow with the -f flag (followed by a file
name), noeshow will store the violated constraints to that file, sorted
by magnitude of violation. If the -n flag is also given, then the sign of
the violation (negative is short) is also saved. So, to save constraint
violation information from our current session to a file named viol.info,
type the fol lowing command:
Command: noeshow -f viol.info noe.cnst
The -f flag works in addition to what noeshow already normally does. This means
that a duplicate set of constraints is now showing. Close the duplicate
set with:
Command: close obj 2
If you wish to see the saved violation information, you can page through
the file with more:
more viol.info
Hitting the space bar will page through the file, and 'q' will quit.
Satisfied constraints*
It is sometimes desirable to see the satisfied constraints as well. First,
remove the current constraints displayed with:*
Command: close obj 1
Then run noeshow with the -a option:
Command: noeshow -a noe.cnst
The numerous satisfied constraints are shown as green lines, with the violated
constraints in their previous colors.
Note that the displayed constraints are in a "graphics object", i.e. a
series of move/draw commands in various colors. The constraints cannot be
referenced via an atom specification, e.g. the command:
Command: show #1 /color=cyan
will not show just the cyan constraints; instead it will have no effect. The constraints
can only be acted on as a whole. For example, they can be undisplayed with:
Command: ~objdisplay 1
and redisplayed with:
Command: objdisplay 1
This completes Exercise 1; you can stop Midas.
Some NMR projects make use of torsion angle constraints and some don't.
If you don't anticipate using torsion angle con straints in your work, you
may want to skip this exercise and proceed with Exercise 3. Exercise 2 uses
files gen erated during the preceeding exercise and therefore you must have
completed Exercise 1 before doing this exercise.*
Noeshow can only use torsion information in one of two formats: AMBER for
mat ( noeshow's "native" format) and X PLOR format (which must be converted,
using a procedure very similar to that for distance contraints). This exercise
uses X-PLOR format constraints, found in the file tors.xplor. The conversion
pro cedure is similar to that for distance constraints:*
xplor2tors tors.xplor > noe.tors
Now start Midas with the model structure:*
midas model.pdb
To show the torsion constraints (along with the distance constraints),
do:
Command: noeshow -A noe.cnst noe.tors
The -A flag causes all torsion constraints to be shown; otherwise only the violated
torsions would have been depicted. The torsion constraints are drawn as
color coded "cages" about the central bond of each torsion. You should probably
scale up the image to get a good look at the various torsions.
The color scheme for the torsions re flects the degree of satisfaction.
The exact meaning of each color depends on whether the torsions were generated
by X-PLOR or AMBER:
AMBER: X-PLOR
Energy penalty of: Dihedral is...
Green 0.0 satisfied and not within 5
degrees of extreme bounds
Yellow <=1.0 satisfied but within 5
degrees of extreme bounds
Orange <=4.0 violated by no more than 10 degrees
Red >4.0 violated by more than 10 degrees
In this model structure no torsions are violated badly enough to be colored
red.
Unlike distance constraints, noeshow does not yet support saving torsion violation information to a file.
You have completed Exercise 2. You may stop Midas now.
At times during NMR structure determination, it is useful to visually inspect
which hydrogens are spatial neighbors of a particular hydrogen or hydrogens
of interest. Though it is quite possible to carry out such an inspection
in Midas Plus without noeshow, noeshow offers features that make such an inspection easier and more direct.
To demonstrate this use of noeshow, first go to the exercise directory
(as per Exercise 1) and open the model struc ture:
midas model.pdb
Now it is necessary to indicate which hydrogen(s) are of main interest,
i.e. which hydrogen(s) we should check for near neighbors. The MidasPlus
mark command can be used to associate a secondary name with one or more
atoms. Associating the name noemark1 with the main hydrogen(s) will indicate
to noeshow that those are the hydrogens of main interest. First, we have to indicate
to MidasPlus that we intend to use the name noemark1 with the command:
Command: makemark noemark1
Let us assume that the main atoms of interest are HG1 and HG2 of residue
27 (glutamic acid). Mark them with:
Command: mark noemark1 :27@HG=
and so we can identify them, color them with:
Command: color cyan /mark=noemark1
We should be all set to go, right? Unfortunately, no. Noeshow is written in a language called perl, which is quite powerful and thereby
greatly reduced the time necessary for implementation. How ever, perl is
not very fast at numerical calculations. Therefore it is best to indicate
exactly which atoms distances need to be calculated to as well as from.
We can do this by marking them with the name noemark2. Let's assume we're
interested in other hydrogens within 5 angstroms of our HG protons. The
commands to mark these other hydrogens are:
Command: makemark noemark2
Command: mark noemark2 /mark=noemark1 za<5.1
This later command marked (with the name noemarkz) all atoms within 5.1
angstroms of the atoms marked with the name noemark1. Now we are ready to
run noeshow. To indicate that we are interested in monitoring H-H interactions of 5 angstroms
or less we use the -h flag like so:
Command: noeshow -h 5
The resulting lines and distances look like a tangle unless we focus in
on the region of interest with the window command:
Command: window /mark=noemark2
Also, it makes examination easier if the center of rotation is centered
in the region of interest:
Command: cofr /mark=noemark2
After examinig the noeshow results, you have completed Exercise 3. You may stop Midas.