The Dock Manual module is available as a part of the Segment Volume package. The module is a Chimera extension module. To use this module, the Segment Menu module of the Segment Volume package is required. You will need the Chimera and EMAN software packages to use this module.
The module helps dock two 3D density maps displayed in Chimera (using rigid body transformations). You can use the mouse to drag and rotate the model or use the GUI to incerement the location and orientation. The GUI also keeps track of the transformation of the model from the starting orientation and position of the model.
Note: This version of the Segment Volume package is a pre-release version.
The module files are stored in the directory DockManual. To list the module under Chimera's Tools menu, add the directory - containing - the DockManual directory to Chimera's list of Tools.
To do so, open Chimera's main window, choose Perferences under Favorites menu, then choose the Tools category and then Add the directory - containing - the DockManual directory. This will list the tool under AIRS on the Tools menu.
To start the module from the Chimera menu, first you will need to ensure that the module is listed under Chimera's Tools menu. Then, click on Dock Manually in the AIRS menu, under Chimera's Tools menu.
Alternatively, you can use the command line tool in Chimera's IDLE tool (under Programming tools on the Tools menu), and type:
>>> import DockManual
>>> DockManual.dockmanual.show_dock_manual_dialog()
The Dock Manual dialog panel has six main sections. The first section is the Input data section. The Data file menu automatically lists available data regions in Chimera's Volume Viewer. The Probe model menu lists all Chimera open models including volume data regions in Chimera's Volume Viewer.
To select an input (volume) data set, simply pick an entry from the Data file menu. The size of the input data set in pixels is automatically displayed on the dialog, below the menu. If the data set is displayed in Chimera, then the Displayed value is set to Yes.
To open new models, click the Open button below the menu. This will open Chimera's Volume Viewer dialog and an Open file browser dialog. After adding the models, if the models are not listed on the data menu, click the Refresh menu button, next to the Open button on the Segment Simple dialog.
Alternatively, you can directly open new models using Chimera's Volume Viewer. Once again, if the newly opened models are not displayed on the data menu, hit the Refresh menu button.
To select an input probe model, simply pick an entry from the Probe model menu. This model is transformed (rigid-body rotation and translation) to fit into the input data.
To open new models, use Chimera's File menu on the Chimera main window to open models (volume data or PDB structures).
You can specify the density parameters of the input data, in terms of the Angstroms per pixel and Resolution. The default values are set to 1.0 for both the parameters.
The Angstroms per pixel value specifies the number of Angstroms per pixel along any given dimension. It is assumed that this value along all the three dimensions (x, y, and z).
The Resolution value specifies the resolution of the structure generated from raw data.
To change the units used to specify translation and rotation, you can check the Units checbox at the top of the dialog. You can choose the units for translation as Angstroms or Pixels and the units for rotation as Degrees or Radians. You can also choose the angle convention to be either EMAN's euler angle convention or Chimera's spin axis convention.
You can specify the transformation to be applied to the probe model using the Probe Transform section. To view the Probe Transform section, check the Transform checkbox at the top of the dialog.
You can choose the angle conventions and the translation and angle units in the Parameter Units section.
The Apply Xform button applies the transform to the probe model. The Set Xform button sets the global transform of the probe model to the specified transform parameters. The Get Xform button gets the current global transform parameters of the probe model.
To move the probe model, you can also use the mouse buttons.
To move the probe model in inceremental steps, you can pick the parameters that you want to change. Here, dx, dy, dz correspond to x, y, z directions respectively, and da0, da1, da2 correspond to the EMAN Euler angles, ds0 corresponds to the spin axis angle.
You can specify the distance/angle you want to change the parmeters by specifying the values in the two boxes next to Step button. The Step button steps the probe model in the chosen directions by the chose amounts.
To view the Optimize parameters and the Optimize optionssections, check the Optimize checkbox at the top. To automatically optimize the docking you can use the Optimize options section. There are two options available in the current release.
The first one, Mean density at C-A, optimizes the density at the Carbon-alpha atoms in the probe atomic structure. This would work ONLY IF the probe model is an atomic model with Carbon-alpha atoms. This method optimizes the density values at all the Carbon-alpha atoms. The search space is specified in the Optimize parmeters section. The units correspond to Parameter units section.
The Get button computes the mean density at all the Carbon-alpha atoms. The Optimize button uses the angle range and angle step size in the Optimize parameters section, and the current position and angles as the starting orientation. The Save button saves the probe model with its orientation relative to the starting orientation of the input probe model.
The second method, Foldhunter, simply calls EMAN's foldhunter program. The search space is specified in the Optimize parmaters section. The units correspond to Paramter units section.
Note that the foldhunter program uses only the current angle parameters as the starting angle parameters of the probe model and the angle step size and angle range. It does NOT use the current position of the probe model as the starting position.
The output data section has an Output data menu that lists the current segmented output files. To open or display the file in Chimera, click on the Show button. If more than one output file was created, then you can click on Show All button to open and display all the files on the menu.
The Hide button closes the model (associated with the file on the Output data menu) in Chimera, but leaves the entry on the Volume Viewer data menu unchanged. The Hide All button applies the Hide button to all the files on the output data menu.
The Remove All button removes all the entries on the Output data menu, but leaves the corresponding entries (if any) on the Volume Viewer data menu unchanged.
The Close button closes the Dock Manual dialog. The Help button opens this help page.
In the first figure, we have the input model (volume density) and a probe model (atomic structure). We make the input model inactive (see Chimera's Model Panel under Favorites). In this case, the input density map has an Angstroms per pixel value of 1.6 and a Resolution of 6.5 Angstroms.
Now, we use the mouse to align the probe model into the input model. Once we have aligned, we can save the probe model with a new orientation relative to the original probe model orientation by clicking on Save button in the Optimize section.
To get even better results, we use the Foldhunter program. We re-load the modified probe model from the previous step and select it on the Probe model menu. We specify an angle range and an angle step size and then call EMAN's foldhunter program by clicking on Apply button next to Foldhunter in the Optimize options section.
To align using the mouse or the dialog, it is best to make the input data inactive. To do so, see see Chimera's Model Panel. After making the input data inactive, you can apply the transformations to the probe model and note the transformation relative to the input data.