THE COMPUTATIONAL CENTER FOR MACROMOLECULAR STRUCTURES
XtalView Release 4.0
The CCMS proudly presents the XtalView version 4.0 which includes many
new features especially in "xfit". This document includes list of new features
definitions and some helpful hints on how to use them. For help in downloading
and installations, please refer to 'README' in the distribution.
DISPLAY environment variable
On DECs with PowerStorm 4D50 graphics, the display might hang if you set
your DISPLAY variable to ":0.0". The workaround is to use the longer form
setenv DISPLAY hostname:0.0
On SGIs you have to set DISPLAY to :0.0 for stereo to work.
Several new features have been added to improve geometry refinement, especially
of the main-chain. The program now has a map of preferred phi-psi geometry,
and can move structure near one of the preferred region into the maxima.
Thus, if a strand is nearly beta it will become more beta in character.
The restraint is soft and acts slowly so as not to whip the model and allow
the bond angles, distances and the petide plane to anneal. The peptide
plane has been made more robust, to make it harder to get it into bad geometry
and to bring it in from farther away. This has been done by adding torsions
to the peptide to keep it planar. In fact the program is now able to flip
a bad peptide plane fully around without user intervention.
The program also attempts to ratchet Chi1 into one of the allowable positions
with a gentle nudge. It is not enough to force them into the position but
does provide a sort of detent to help keep them in this region if the geometry
of the residue is moved. The relative weight of the new torsions is controlled
by a slider, Torsion Weight, which has been added to the refine window.
The restraints have large sigmas (except omega the peptide plane) but can
be made more aggressive by increasing their relative weight with the slider.
Main-chain hydrogen bonds are now searched for and added to the restraint
list. This helps regularize secondary structure and anchors the refined
bit relative to the rest of the structure. Only main-chain to main-chain
bonds are used. Others can be still be added by hand for particular trouble
spots. Four macro commands have been added to simplify setting up geometry
refinements. While they don't add any functions that weren't already in
xfit they do make it much simpler to set up a refinement of a range of
Refine Region - the focus residue and its two neighbors are refined one
cycle. They are left in refine mode and pressing the space does another
round of refinement. This can be repeated until the semi-colon key is used.
Refine Fragment - this command is identical to the previous except that
the entire fragment containing the focus residue is refined.
Refine Range - as the previous two except that it refines the range between
the top two atoms on the stack; that is, the last two picked.
Refine while Fitting Range - Similar to above except that the range is
put into background refine mode so that it is continuously updated as you
continue to work. If you click on an atom it will be made active so that
you can move it with the middle mouse button and the rest of the model
will follow along. Thus you can nudge residues into density and influence
the refinement by clicking on atoms. Hints: It helps to rotate the viewpoint
such that the atom movement desired is close to the plane of the screen
- avoid shortening bonds as this adds a lot of energy to the model and
may distort it in ways you did not intend. Also you can anneal the model
by gently shaking an atom and transmitting the movement to the rest of
the model. If the map is good this is especially effective.
In all of these modes the map is taken into consideration in the refinement
by trying to maximize the density around the atoms. This works very well
at higher resolutions where the map starts to take on some atomic character.
At lower resolutions the map looks less like an atomic model. To compensate
for this, the weight of map is adjusted according to the resolution of
the map. The map used is the one set on the refine window. If you have
more than one map, you can set the map on this window to be refined against.
If you have a map(s) loaded but want it ignored, then set the refine map
number to an empty slot.
Model window - controls to allow limited atom editing
have been added.
You can now delete an atom by highlighting it and then selecting Delete
Atom. This is probably best used with caution, but it's especially nice
to get rid of unwanted hydrogens. You can also edit the B-value and/or
occupancy by changing the values and then pushing the replace button. The
Go To button has been moved next to the name field, to better show their
relationship. You can type a name of a residue in and then press the Go
To button to center it on the screen. Alternatively, you can select it
in the scrolling list and then press Go To. A model number field has been
added to the window at the top that mirrors the number on the main window
to make it easier to flip between models.
Dictionary - A load dictionary feature has been
added that allows changing the dictionary without having to remember its
name and going to the file window. You can add one of the standard dictionaries:
No H dictionary
Polar H dictionary as in XPLOR
All H dictionary
If the conformer function is not working you probably have a dictionary
that doesn't match the residue. You can quickly remedy this on the model
Error Window - the Go To Next Error button now works
as advertised. In addition there is a button to deep-six an error by deleting
the residue in question. If the residue is not a water then you are asked
if you really want to do this. It can be undone on the Model Window by
toggling the delete flag. There is also a Fit Error button to put the residue
into fitting mode and let you fix the residue. Lastly, an Examine Active
Model button has been added that compares the model to ideal geometry and
lists any residues and the reason why they are suspect.
SHELX features - the program reads SHELX LIST 6 (CIF)
format .fcf files. The program has been able to read LIST 5 format but
LIST 6 has become the SHELX standard. The program also now reads and writes
ANISOU cards in the PDB file. These contain anisotropic B information.
These are not just a SHELX feature, but we don't know of any other software
that uses them.
Maps - 2 new maptypes have been added that use Sigma-A
2mFo-DFc and mFo-Fc. These map types calculate sigma-A coefficients on
the fly from Fo and Fc. Thus if you do an omit map calculation the omit
map made with mFo-DFc will use the Fc-omit values. We have found the Sigma-A
maps better at reducing phase bias than other map types. Using the shake
option and sigma-A maps is about as good as it comes in removing phase
bias. If you have figure-of-merits in the Fc column then the program will
not do the sigma-A calculation as this would be an error. If you have a
model you can replace the figure-of-merits with Fc's by using the Calculate
All and Scale button on the SfCalc window and then you can use the sigma-A
Anisotropic B's (U's)-
In the view window there are three new features for viewing anisotropic
B's. They will also work with isotropic B's - the program converts the
B into the equivalent U matrix. With thermal Axes on the View window, you
can see the direction and magnitudes of the thermal vibrations. With Thermal
Ellipse, a probability surface is calculated and made into a vu object.
The percent probability is controlled by a slider near the other two options.
If no ellipse shows up for an atom, then its U values form a on-positive
definite solution and it is ignored. This is fairly common in the beginning
stages of an anisotropic refinement but if it doesn't go away it needs
to be dealt with. SHELX also lists these atoms in its output. The thermal
ellipsoids should change evenly and be correlated along bonded atoms. Using
this option, you can quickly spot outliers with a little practice for the
eye. It is instructive to see how large the 50% probability ellipse is
for a water with a B-value of 100.
A new Water Window has been added that is used to automatically hydrate
maps and rename waters according to another model.
Automatic hydration - First you need a map to add waters to, and a model
to which the waters will be appended. The map should be a difference map;
other map types can be used but they will take a lot longer to search.
The user sets two parameters: the minimum density to consider and the maximum
number of waters to add. The water addition algorithm is as follows. First
all the peaks in the map in one asymmetric unit are found. These are then
sorted by size, largest first. The program looks at each peak in turn and
determines if it is not overlapping with the current model or with a symmetry
mate of the current model. It then considers if the peak is close enough
to the model to hydrogen bond. If all these criteria are met, then a water
is added at the end of the model. The added water is then real-space refined.
This continues until either the peak list is exhausted or the maximum number
of waters to add is reached.
Rename Waters - This renames the waters in the active model according to
the waters in another model. If the active model contains a water close
to one in the second model, then the active model water is renamed to match.
After all the waters have been looked at, any waters that didn't match
are renamed sequentially from the name of the last match found. Use this
command to make the names of waters in two models match. This is especially
useful for mutant structures. Assume you have just finished adding waters
to a mutant protein structure. Load the wild-type model. Make the mutant
the active model, and set the Rename As In # field to the number of the
wild-type model and issue the command.
Least-Squares Plane - This command calculates
a least-squares plane for all the atoms on the stack. To use it, first
clear the stack on the main window and then click on all the atoms to be
in the plane. Then issue the command. To get the distance from this plane
for any atom, click on the atom to place it in the stack and then issue
the Distance From Plane command.
Spline map - Maps can be represented by spectral spline
approximation to the continuous function giving the density. The spline
option makes all references to electron density slower, but makes density
interpolation very accurate, allowing accurate contouring on a different
grid without re-FFTing, and better-informed refinement.
Raster3D interface - New option in xfit provides
an interface to the Raster3D. Raster3D is a software package for generating
photorealistic images, written originally by David Bacon and now maintained
by Ethan Merrit at http://www.bmsc.washington.edu/raster3d.
The output generated from this interface produces the input to the Raster3D
program, "render". The options include the image size which may either
be "Full Screen" or "same as canvas", "Ball & Stick" by default or
"space-filling models", "Distance" which controls the perspective and "Primary
light source" which can be set to any eight positions.
note: If you will be using XV with tiff option, make sure your "Raster3D"
was built with TIFF library as stated in the Raster3D INSTALL document.
The TIFF library can be obtained from sgi.com
if your system doesn't already have one.