| Xsight |
The Xsight package is used to analyze X-ray diffraction data from macromolecular crystals. All areas of structure analysis are included from phasing to model fitting to visualization. Xsight encompasses components of the programs Insight II, XtalView, MADSYS, REPLACE, CNX, ProLSQ95, and RotLSQ to provide a rich library of crystallographic tools. You can use the Insight II program to launch all the programs within the package.
The crystals and projects paradigm of the XtalView package has been adopted overall for the Xsight package. This paradigm defines a very easy and convenient way of organizing and managing the data analysis that a macromolecular crystallographer typically performs.
The management system is organized around two distinct concepts. First, it recognizes that macromolecular crystallographers are often working on more than one structure simultaneously. This fact is taken into account by using a crystal file for each structure that is being worked on. A crystal file contains the basic crystallographic information that is needed to perform crystallographic calculations: unit cell parameters, space group, crystallographic symmetry operators, and non-crystallographic symmetry operators.
Secondly, the system recognizes that macromolecular crystallographers work with many data sets and follow many paths in solving a protein crystal structure. The concept of project is used to organize this type of work. A project is defined by a working directory pathname and a crystal file. When working on the same crystal structure, "project" just defines the working directory where your data are stored.
A special directory is created for storing the crystal and project information. This directory is referenced by the environment variable $CRYSTALDATA and contains two main database files named projects and crystals.
The projects file contains two records for each project. The first record is a title that identifies the project and the second record contains both the pathname of the project working directory and the crystal file that is appropriate for this project.
The crystals file contains one record for each individual crystal file. That record contains only the name of the crystal file. Each crystal file that is listed in crystals is also located in the $CRYSTALDATA directory. By convention, crystal files do not have file extensions.
The $CRYSTALDATA directory should be used only for storing crystal and project information. In the following simple example, The $CRYSTALDATA directory contains the following four files:
The crystals file contains two records,
cvccp sirhp
which are the filenames for the two crystal-type files that are located in $CRYSTALDATA. The sirhp file has the following records:
name hemoprotein subunit
cell 69.75 77.44 87.79 90.0 90.0 90.0
spgp P2(1)2(1)2(1)
symm x,y,z; 1/2-x, -y,1/2+z; ...
The example projects file contains a description for two projects and thus four records:
cvccp_deriv_1
/usr/people/pns/project_1 cvccp
cvccp_native
/usr/people/pns/project_2 cvccp
where the first record for each project is the title. and the second record contains the pathname of the working directory and the crystal filename.