Sphgen Sphere Files

Chimera can read and write spheres in the format produced by the DOCK accessory program sphgen. DOCK uses the sphere centers as points for placing ligand atoms. Chimera can be used to edit sphere clusters from sphgen and to save edited clusters or sets of atoms as spheres. See also: Write DMS, Dock Prep, ViewDock

The sphgen input type is indicated by the filename suffix .sph or by using prefix:filename in the command line, where prefix is sph.

The small example file 12123.sph contains only one cluster, whereas sphgen output generally contains multiple clusters, including a “cluster” number 0 with all of the spheres. Chimera loads each cluster as a molecule model and its spheres as atoms, with sphere radii read from the file. Clusters are assigned unique colors, and cluster 0 (if present) is hidden automatically.

Cluster models are listed in the Model Panel and can be manipulated in the same ways as other molecule models. Clusters read from the same sphere file are assigned the same model number but sequential submodel numbers, which are not necessarily the same as the cluster numbers given in the file. For example, if a sphere file containing clusters 0, 1, and 2 is opened as model 1, cluster 0 will be model #1.1, cluster 1 will be model #1.2, and cluster 2 will be model #1.3. However, the names of the models will reflect the cluster numbers given in the file.

Editing Sphere Clusters

Entire clusters (models) can be closed, and individual spheres can be selected, displayed/undisplayed, and deleted like ordinary atoms. For selecting, picking from the graphics window or with Select... Zone may be especially useful. Just the displayed and/or selected spheres (atoms) can be saved. Conversely, unwanted spheres can be deleted or undisplayed before the others are saved.

Clusters can be merged using the copy/combine function in the Model Panel or the command combine.

Saving Sphere Files

The dialog for saving a sphere file can be invoked with save sphgen in the Model Panel. This function is only available after a sphere file has been opened. Users lacking a sphere file but who wish to save atomic coordinates (such as a ligand in the binding site) as spheres can open the example file 12123.sph in Chimera to enable sphere-saving. If atoms are saved as spheres, their VDW radii are used as the sphere radii.

Individual models or blocks of models can be chosen from the Save models list with the left mouse button. Each chosen model will be written as a cluster.

Options:

• Save displayed atoms only - only write coordinates of atoms (spheres) that are displayed
• Save selected atoms only - only write coordinates of atoms (spheres) that are selected

• Use untransformed coordinates - write coordinates without applying any rotations and translations that have been performed in Chimera. This is recommended for spheres, and is equivalent to writing a model relative to itself (see the multiple-model case below).

• Save relative to model [model] - save coordinates relative to the untransformed coordinates of a specified reference model (otherwise, transformed coordinates will be saved). This is useful for preserving the spatial relationship between models. In most cases, spheres should be written out relative to their original input model.