[ ICM Convert | Optimize | Regularization | Edit Structure | MMFF | Minimize | Sample Loop | Stack | Energy Terms ]

3.16.1 ICM Convert

To calculate energy, build a molecular surface and for all energy operations you need to convert a PDB file into an ICM object.

• MolMechanics/ICM-Convert/Protein
• Select the object you want to convert from the drop down list.
• Check or uncheck the options, delete water, optimize hydrogens, replace the original, and/or display the result.

To convert a small molecule into an ICM object.

• MolMechanics/ICM-Convert/Chemical
• Select the ligand.
• Choose whether you want to keep the current geometry of the ligand or not.
• Check or uncheck the options build hydrogens, fix amide bonds, and/or overwrite geometry.

3.16.2 Optimize H,His,Asn,Gln,Pro

This option optimizes H, His, Asn, Gln, and Pro by maximizing hydrogen bonds and other interactions with the rest of the protein and/or with the ligand.

To perform this optimization

• Convert your protein to an ICM Object.
• Select MolMechanics/Optimize, H, His,Asn,Gln and Pro
• Choose whether you want to sample rotatable hydrogens or optimize His, Asn and Gln.

3.16.3 Regularization

This option is described in detail in the modeling chapter here.

3.16.4 Edit Structure

Set Bond Type

• Select the two atoms forming the bond.
• MolMechanics/Edit Structure/Set Bond Type
• Choose the Bond Type from the drop down arrow.
• Press Apply button

Set Formal Charge

• Select the atom.
• MolMechanics/Edit Structure/Set Formal Chage
• Choose the Charge from the drop down arrow.
• Press Apply button

Set Chirality

• Select the atom.
• MolMechanics/Edit Structure/Set Chirality
• Choose the Chirality from the drop down arrow.
• Press Apply button

Build Hydrogens

• Select the atoms.
• MolMechanics/Edit Structure/Build Hydrogens
• Press Apply button

Set Tether

Theory

A tether is a harmonic restraint pulling an atom in the current object to a static point in space. This point is represented by an atom in another object. Typically, it is used to relate the geometry of an ICM molecular object with that of, say, an X-ray structure whose geometry is considered as a target. Tethers can be imposed between atoms of an ICM-object and atoms belonging to another object, which is static and may be a non-ICM-object. You cannot create tethers in ICM-Browser, however, if the project that you have loaded contains tethers between two objects, then they can be displayed:

• Convert the two structures you wish to tether to an ICM object.
• MolMechanices/Edit Structure/Set Tether
• Right click on the first atom you wish to tether and click on the first option which is the selection language for the atom. This information will automatically be placed in the first atom dialog box. Alternatively you can type in the ICM selection language into the dialog box.
• Right click on the second atom (in a different object) you wish to tether and click on the first option which is the selection language for the atom. This information will automatically be placed in the second atom dialog box. Alternatively you can type in the ICM selection language into the dialog box.
• Press Apply button

Delete Tether

• Select the atoms you wish to delete the tethers from.
• MolMechanices/Edit Structure/Delete Tether

3.16.5 MMFF

Set Types This option is described in detail here in the command line manual http://www.molsoft.com/man/icm-commands.html#set-type-mmff

Set Charges This option is described in detail here in the command line manual http://www.molsoft.com/man/icm-commands.html#set-chargemmff

Read Libraries This option is described in detail here in the command line manual http://www.molsoft.com/man/icm-commands.html#read-librarymmff

3.16.6 Minimize

Cartesian This option is described in detail here in the command line manual http://www.molsoft.com/man/icm-commands.html#minimize-cartesian

Local This option is described in detail here in the command line manual http://www.molsoft.com/man/icm-commands.html#minimize

3.16.7 Sample Loop

This option is described in the Loop Modeling section.

3.16.8 Stack

Operations which use the ICM Biased Probability Monte Carlo method e.g. docking and loop modeling generate a stack of energy conformations.

MolMechanics/Stack/View will display the conformations of a stack in a table ranked by energy. Each conformation can be viewed by double clicking on the table. A stack file will have the extension .cnf. For example, after running the sample loop algorithm a stack of different loop conformations will be generated.

MolMechanics/Stack/Play This option will play the elements of the stack as a movie. You can set the number of frames for the movie and also select whether you would like ICM to interpolate between each frame. You can save this movie in avi, mpeg format using the Screen-Grabbing Movie options.

MolMechanics/Stack/Add current conformation This option will add the currently displayed conformation to the stack. This is useful for experiments such as multiple receptor docking whereby you dock to a stack of conformations.

MolMechanics/Stack/Store Stack in Object This option takes the current stack and stores it in a compressed form inside the specified object. The compressed stack can then be extracted with the load stack object command. Option stack of the montecarlo command stores the generated stack inside the current object automatically.

MolMechanics/Stack/Delete Deletes the current stack.

MolMechanics/Stack/Set conf Comparison This option compares the stack as described here: http://www.molsoft.com/man/preference.html#compareMethod and http://www.molsoft.com/man/icm-commands.html#compare

MolMechanics/Stack/Recalculate Energies Recaluclates the energy of a current stack if changes have been made.

3.16.9 Energy Terms

The energy function calculated for any conformation of an ICM molecular object consists of individual terms described which can be turned on and off using MolMechanics/Energy Terms. These terms are described in more detail here http://www.molsoft.com/man/terms.html