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THE COMPUTATIONAL CENTER FOR MACROMOLECULAR STRUCTURES

XtalView Release 3.2

December 3, 1997




The CCMS proudly presents the XtalView version 3.2 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 for DISPLAY:
setenv DISPLAY hostname:0.0
On SGIs you have to set DISPLAY to :0.0 for stereo to work.


New Xfit features

Geometry refinement

Model window controls atom edition

Load dictionary in model window

Error Window-improved

2 new map types that uses Sigma-A coefficients

SHELX file read

Water - hydrate maps and rename waters

Least-Squares Plane

Spline map - maps represented in spectral spline approximation

Thermal Ellipses in view window

Raster3D interface


Geometry refinement:
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 residues.

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:

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 window now.

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 coefficients:
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 maps.

Anisotropic Bos (Uos)-
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.

Water -
A new Water Window has been added that is used to automatically hydrate maps and rename waters according to another model.


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.