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Ligand

Entry Types

Moloc has various entry types which are grouped in two main classes, 2- and 3-state entries

2-State Entries

These have two states visible and invisible. The user can switch between those in the menu item 'm' of the display menu (... or .). There, a list is presented of all entries currently in memory. Each item of this list has a visibility indicator field followed by: letter: 'name of entry' The letter indicates the type of entry:

3-State Entries

These entries are more directly part of the modeling activity and have in addition an active state. They are handled in menu item 'a' of the display menu.

Ligand Modification

In the file format .pdb, atoms carry various items of information which characterize the monomer they are part of (monomer code, sequence number, insertion code, etc.). This information is carried along within Moloc and allows to write back correct .pdb files. Heterogen items (ligands) also carry such information, which is, however, not standardized as for amino- or nucleic acids. This may cause problems as soon as a heterogen is modified. Such problems can be avoided by following the procedures given below, which are exemplified with the ligand methotrexate of the structure 4dfr.pdb.

Read Ligand as Separate Moloc-Entry

In case that the .pdb file has no directory (SEQURES, HET records) the whole file is packed in a single Moloc entry. Separation of ligand and rest can then be achieved by reading in the structure twice and deleting the ligand in one structure and the rest in the other.
Entries read from a .pdb file are automatically classified as polymers (p, see above). For single heterogens this makes little sense and may interfere with further handling in Moloc.

Delete Monomer Information of Ligand

Modify Ligand

Now, when modifying the ligand entry, Moloc does not try to generate monomer information or monomer-specific atom names. Also, when combining various entries, make sure all of them are free of monomer information. Such information must only be provided in a final step, in which the modified ligand is united again with the rest-entry.

Write back Modified Ligand in .pdb-Format

It is advisable to keep the ligand as molecule-entry in Moloc as long as modification work goes on. The .cif file format allows to recover it as such in future sessions. Only when a final structure must be available in .pdb format the following steps must be performed.