Open (Read) Molecule File via the Menubar

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Tripos Bookshelf > SYBYL Basics > Open and Save Files of Molecules > Open (Read) Molecule File via the Menubar

5.1 Open (Read) Molecule File via the Menubar

File > Open

Open File

Directory

Current directory. Click the down arrow to display and select from a pull-down list of parent directories.

Icons

The icons to the right of the Directory field perform the following operations (descriptions are from left to right):

Go back to the previously selected directory.
Go up one level in the directory tree (i.e., the parent directory).
Delete the selected file(s) in the list.
Create a new folder/directory within the current directory.
Display additional information about this dialog.

Bookmarks

Provides quick access to commonly used directories. By default, the directory in which you started SYBYL ([$CWD]), your home directory ([$HOME]), and SYBYL's demo directory ([$TA_DEMO]) are listed. If the default directory is changed from within SYBYL, [$PWD] will also be listed.

To add another directory to the list (e.g., a local copy of the PDB database files), navigate to that directory, either through the Directory pull-down or by typing directly into the File to read field (and pressing OK). Press the green "+" button.
To remove a directory from the list, click that directory and press the red "-" button. (Note that the default bookmarks cannot be removed.)
User-defined bookmarks are stored and can be directly edited in the $HOME/.sybyl/directory_bookmarks file.
Note: To resize the list of bookmarks, click on the bottom border of the list and dragging it up or down.

Molecule Areas

List of molecule areas and name of any currently displayed structures. Click a molecule area in the list to select it. By default, SYBYL automatically selects the first available molecule area. If multiple files are selected, molecules are loaded in consecutive molecule areas.
Click in the list area and drag the cursor to scroll left or right.
(Note that there are cases when this list is disabled, for example, when opening a database (File > Database > Open)).

Directory Navigation

List of subdirectories in the currently selected directory. Click an item to open it. The selected directory's name now appears in the Directory field and the Directory Navigation and Selection lists update to show its contents. Select [Parent] to move up one level in the directory tree.

Selection

Items in the currently selected directory that match the Files of Type selection are listed. Select one or more item(s) from the list.

File to read

The path and name of file(s) to load. Type a subdirectory name or a full directory path and press OK to open that directory. Type the name of the file and press OK to open that file.
For MDL SD or MOL files, normalization (aromatization and standardization) of the structures is done by default. To control this default behavior, use the Tailor variable TAILOR!TABLE!MDL_NORM_AROM.
The label for this field varies depending on how this dialog was invoked. For example, if the dialog was displayed using File > Database > Open, this field is labeled Databases.

Files of Type

The type of files to display in the list.

Molecule--Files containing molecules (e.g., .mol2, cry, .pdb, ...). Selected file(s) will be loaded into molecule areas. If a file contains multiple molecules, the Multi-Mol2 File Detected dialog is displayed asking whether to load the contents into an MSS or molecule areas.
SYBYL Mol2--All .mol2 files. Selected file(s) will be loaded into molecule areas. If a file contains multiple molecules, the Multi-Mol2 File Detected dialog is displayed asking whether to load the contents into an MSS or molecule areas.
SLN--Files containing SLNs (e.g., .sln, .hits). Selected file(s) will be loaded into MSSs, one for each file.
MDL-SDF--All MDL SD files (e.g., .sdf, .sd). Selected file(s) will be loaded into MSSs, one for each file.
PDB--Files containing proteins (e.g., .pdb, .ent, ...). Selected file(s) will be loaded into molecule areas.
Sequence--Files containing sequences (e.g., .pir, .fast). Selected file(s) will be loaded into molecule areas and displayed the Sequence Viewer.
Spreadsheet--All table files (e.g., .tbl, .tsv, .csv, .hits). Selected file(s) will be loaded into MSSs, one for each file.
Database--Database files (e.g., .tdb, .mdb). Selected file(s) will be loaded into MSSs, one for each file.
Any File--Files in the current directory. SMILES files can be selected and opened using this option.
Other options may appear in this pull-down depending on how this dialog was invoked and the type of object that is being opened.

Directory	Current directory. Click the down arrow to display and select from a pull-down list of parent directories.
Icons	The icons to the right of the Directory field perform the following operations (descriptions are from left to right): Go back to the previously selected directory. Go up one level in the directory tree (i.e., the parent directory). Delete the selected file(s) in the list. Create a new folder/directory within the current directory. Display additional information about this dialog.
Bookmarks	Provides quick access to commonly used directories. By default, the directory in which you started SYBYL ([$CWD]), your home directory ([$HOME]), and SYBYL's demo directory ([$TA_DEMO]) are listed. If the default directory is changed from within SYBYL, [$PWD] will also be listed. To add another directory to the list (e.g., a local copy of the PDB database files), navigate to that directory, either through the Directory pull-down or by typing directly into the File to read field (and pressing OK). Press the green "+" button. To remove a directory from the list, click that directory and press the red "-" button. (Note that the default bookmarks cannot be removed.) User-defined bookmarks are stored and can be directly edited in the $HOME/.sybyl/directory_bookmarks file. Note: To resize the list of bookmarks, click on the bottom border of the list and dragging it up or down.
Molecule Areas	List of molecule areas and name of any currently displayed structures. Click a molecule area in the list to select it. By default, SYBYL automatically selects the first available molecule area. If multiple files are selected, molecules are loaded in consecutive molecule areas. Click in the list area and drag the cursor to scroll left or right. (Note that there are cases when this list is disabled, for example, when opening a database (File > Database > Open)).
Directory Navigation	List of subdirectories in the currently selected directory. Click an item to open it. The selected directory's name now appears in the Directory field and the Directory Navigation and Selection lists update to show its contents. Select [Parent] to move up one level in the directory tree.
Selection	Items in the currently selected directory that match the Files of Type selection are listed. Select one or more item(s) from the list.
File to read	The path and name of file(s) to load. Type a subdirectory name or a full directory path and press OK to open that directory. Type the name of the file and press OK to open that file. For MDL SD or MOL files, normalization (aromatization and standardization) of the structures is done by default. To control this default behavior, use the Tailor variable `TAILOR!TABLE!MDL_NORM_AROM`. The label for this field varies depending on how this dialog was invoked. For example, if the dialog was displayed using File > Database > Open, this field is labeled Databases.
Files of Type	The type of files to display in the list. Molecule--Files containing molecules (e.g., .mol2, cry, .pdb, ...). Selected file(s) will be loaded into molecule areas. If a file contains multiple molecules, the Multi-Mol2 File Detected dialog is displayed asking whether to load the contents into an MSS or molecule areas. SYBYL Mol2--All .mol2 files. Selected file(s) will be loaded into molecule areas. If a file contains multiple molecules, the Multi-Mol2 File Detected dialog is displayed asking whether to load the contents into an MSS or molecule areas. SLN--Files containing SLNs (e.g., .sln, .hits). Selected file(s) will be loaded into MSSs, one for each file. MDL-SDF--All MDL SD files (e.g., .sdf, .sd). Selected file(s) will be loaded into MSSs, one for each file. PDB--Files containing proteins (e.g., .pdb, .ent, ...). Selected file(s) will be loaded into molecule areas. Sequence--Files containing sequences (e.g., .pir, .fast). Selected file(s) will be loaded into molecule areas and displayed the Sequence Viewer. Spreadsheet--All table files (e.g., .tbl, .tsv, .csv, .hits). Selected file(s) will be loaded into MSSs, one for each file. Database--Database files (e.g., .tdb, .mdb). Selected file(s) will be loaded into MSSs, one for each file. Any File--Files in the current directory. SMILES files can be selected and opened using this option. Other options may appear in this pull-down depending on how this dialog was invoked and the type of object that is being opened.

Default Molecule Names

TAILOR!MOL!AUTO_NAME