Volume 2 Chapter 10 Search Menu SAVE MODEL

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SAVE MOL2

Function

SAVE MOL2 is used to specify that a MOL2 file should be written, containing all kept hits for which crystal coordinates are available.

Basic QUEST Procedure

Type SAVE MOL2. See SAVE for more information about use of this control command in Basic QUEST.

Remarks

MOL2 is a file format that provides a complete representation of a molecule for use with software from Tripos Inc. (including SYBYL). Details of the format can be found in documentation from Tripos Inc.

MOL2 files generated by SAVE MOL2 contain the following records:

MOLECULE
ATOM
SUBSTRUCTURE
BOND
CRYSIN

SYBYL atom types are deduced by analysing CSD connectivity information.

For some entries that are not perfectly matched, it is difficult to determine accurate SYBYL atom and bond types. Such entries are indicated by the following comment in the MOLECULE record:

Generated from the CSD - Atom/bond types may be wrong (imperfect match)

For entries with no crystal connectivity, the MOL2 representation will not contain a BOND record. Such entries are indicated with the following comment in the MOLECULE record:

Generated from the CSD - Crystal connectivity not present

The output file will have an extension .mol2.

Graphics QUEST3D Procedure

This facility may be toggled on and off via the MOL2 command in the SEARCH menu or the SAVE-MOL2 command in the QUEST... sub-menu.

Related Command

INFO

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Volume 2 Chapter 10 Search Menu SAVE POSTSCRIPT.