Molecular structures are held in various applications. The files containing data on these structures use formats that are different from the MSF format. The Import and Export functions in the File menu allow you to read and write external file formats to and from QUANTA. Imported files usually require a certain amount of processing before they can be used in calculations such as CHARMm energy calculations. This can be done using the Split and Clean function.
The Import function allows an external file format to be read into QUANTA, creating an MSF and displaying its associated structure. The MSF is assigned the same name as the external file, and QUANTA automatically adds the extension .msf. An external file format can also be read into the MSF of a structure that is currently displayed.
The Export function reverses the import process, allowing structures in MSFs to be converted to the appropriate format and read into an external database.
The Split and Clean function on the Edit menu facilitates adding hydrogens and assigning atom types and bond orders using tools appropriate to various classes of molecules.
Formats that can be handled by QUANTA include:
Although a standard process is used to create an MSF, the actual steps may vary depending on the format that is selected. Selection criteria may be manually or automatically specified at the time the MSF is created.
Several conditions may require special handling when a PDB file is imported. If this happens, QUANTA displays a dialog box asking you to choose what should be done. For example, if the crystallographic spacegroup is missing, QUANTA asks you to confirm that it is. Or, in the Brookhaven standard format, a character in column 17 is an alternate position indicator, but some programs create "pdb" files treating this field as part of the atom name. So correct interpretation of the data requires you to have some knowledge of the provenance of the file. However, for genuine Protein Data Bank files, the import process can be simplified by turning off some or all of these prompts and assuming that the data is in the standard format. This can be done by selecting PDB Import/Export from the Preferences menu and turning on some or all the toggles. During subsequent PDB importation, if any of the conditions arise, a message is output to the textport.
Additionally, during both import and export, atoms may need to be renamed to match a format's conventions. To automatically rename PDB files, display the Preferences menu and select PDB Import/Export. In the Automatic PDB File Renaming Options dialog box, the standard options for import and export, respectively, are:
Change to QUANTA Standard Names
Change to IUPAC/Brookhaven Names
Some PDB files contain multiple conformers - usually as a result of NMR structure determination. By default, QUANTA reads the first conformer and creates an MSF containing this structure. If you turn on the Prompt for Multi-MODEL options toggle in the PDB Import/Export Preferences dialog box, then, whenever you import a file containing MODEL records, you are prompted to choose which conformer should be used to create the MSF and also whether to create a .csr file containing the coordinates of all conformers. The .csr file can then be used in the Analysis application.
You can create an .msf from any single structure in a Protein Data Bank file that contains more than one model. For Protein Data Bank files that contain conformers, you also can create a .csr file to contain all the conformers (see above).
1. Select PDB Import/Export from the Preferences menu. The Automatic PDB File Renaming Options dialog box is displayed:
2. Check Prompt for Multi-Model options, then click OK.
3. Select Import from the File menu. A File Librarian is displayed:
4. Select the file you want to import and the Protein Data Bank format (the default selection), then click Import. A dialog box with multi-model file options is displayed:
5. Indicate the model number you want to import and check the check box if you want to create a .csr file for all the models in the Protein Data Bank file. Then click OK. The file is imported. If there are any nonstandard atom types in the file, QUANTA prompts you to choose options for typing the atoms.
The function Import Multiple PDBs on the File menu facilitates importing several PDB files at a time. All the prompting described above is suppressed during this operation. A dialog box similar to that used for opening MSFs is displayed, allowing one or more PDB files to be selected. These can be all standard Brookhaven format or all CNX/X-PLOR/CHARMm style. The resulting MSF files can replace any currently open MSF file or be appended to it.
Structures imported from external sources, for example, Protein Data Bank (PDB) files, frequently need some editing prior to further work within QUANTA. The files may contain a variety of different chemical entities (protein, solvent, nucleic acid, ligands, ions) for which different editing tools are most suited. For instance, amino acids can have names standardized, forcefield types and bonds correctly assigned, and hydrogens added by means of tools in the Protein Design application which uses templates for these structures. Ligand molecules within PDB files more often need manual editing to generate correct bonding and atom types; this can be done quickly and easily within the Molecular Editor, especially if the ligand is treated alone rather than as part of the entire protein-ligand complex.
Split and Clean on the Edit menu facilitates such operations. It provides a straightforward method for dividing a structure into its constituent parts and the tools necessary for editing each part.
On entering this function, each residue within the structure is automatically classified as protein, solvent, nucleic acid, or other and colored accordingly. You may add extra classifications (e.g., ligand, ions) and can reassign residues or whole segments. A pickable color-coded legend appears in the top right corner of the molecule window.
This tool toggles between coloring the structure according to the classification of each residue and the normal color selection.
This tool can be used to return to the default classifications set by the program.
Operates on residues classified as other, making a new classification for each segment.
Before using this tool, click the desired classification from the legend, denoted by a star. When the tool is turned on, you are prompted to click the residue(s) that are to become this type. Clicking the tool again turns it off.
As above, but reclassifies an entire segment.
A dialog box is displayed which contains a scrolling list of the residue types within the system. One or more can be selected to be reclassified.
Undoes the last change to the residue classifications.
Displays a dialog box in which you can indicate the name of an additional classification.
Displays a dialog box containing the editable names of all the existing classifications, each of which must be unique.
Once residue classification has been performed to your satisfaction, use this tool to create a separate MSF for each classification, the name of which is the original root name followed by an underscore and the class name.
Returns to the original MSF (as it was when the function was first entered).
Once the system consists of MSFs, each containing one type of residue (i.e., after the use of Split and Clean or immediately, if the function is entered with a set of such structures), the tools that facilitate cleaning the structure are enabled. The file protein_structure.gsd holds the definitions used to clean the protein.
Displays a dialog box that allows you to choose which hydrogen representation should be applied - Polar, All, or None.
Operates on any active MSFs that consist entirely of residues recognized as amino acids or classified as protein. The clean process includes:
If the structure contains disordered atoms, gives you the choice of whether to retain them or to keep just one set.
Atom names are changed to conform to the standard amino acid nomenclature as defined in the protein template files ($HYD_LIB/protein_structure.gsd).
Ensures all terminal atoms are present and correct.
If the residue is missing atoms, these are added using the standard amino acid templates, but given an occupancy of zero.
Hydrogens are added or deleted according to the choice set in the Clean Options dialog
At the end of this operation, the atom types should all be correctly assigned.
Connectivity and bond orders are assigned.
Some external programs output solvent with more than one molecule per residue. This tool operates on active residues recognized or classified as solvent and makes sure they have one molecule per residue.
Acts on active residues recognized or classified as solvent. It adds hydrogens as specified by the Clean Options dialog, adjusts atom types, and corrects bonding.
For those structures for which QUANTA does not have template information, it is often necessary to go through the process of assigning correct bond orders and/or atom types (one must be correct before the program can determine the other accurately) and adding hydrogens. The Molecular Editor has a complete set of tools designed to do this, particularly aimed at small molecules rather than proteins. This tool in the Split and Clean palette first asks you to select one MSF on which to work and then takes this alone into the Molecular Editor. This is much more efficient than taking in a whole protein-ligand complex.
Structures built within QUANTA by ChemNote or the Molecular Editor itself should not need further editing here.
Attempts to automatically take a chosen MSF through the Molecular Editor to generate bond orders and atom types and to add hydrogens. Whether this operation is successful critically depends on the initial quality of the structure, i.e., whether it has good enough geometry to determine bond types correctly or if has been typed properly beforehand via dictionaries. An explanatory dialog box is displayed before the edit is attempted. It is up to you to decide whether it would be better to clean up the structure manually.
Operates on all active residues classified as nucleic acids. Atom types are assigned using the standard nucleic acid dictionaries, hydrogens are added, retyping is performed as required, and bond orders are determined from these types.
Quits the Split and Clean palette and restores the MSF(s) as they were before entry.
Exits the palette, retaining the new or corrected MSFs.
The Export function allows structures in MSFs to be converted to the appropriate format and read into an external database.
Complete the following process to export a file using the PDB format.
From the File menu, select Export, and a File Librarian dialog box opens.
Select 1crn.msf from the scrolling list.
Atoms to export: All Atoms from MSF
Rotation transformations: Discard
2. Append remarks to the structure file.
In dialog boxes that offer the opportunity to enter remarks, enter no more than one line of text per dialog box.
Select the OK button, and the .pdb file is generated.