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:
- m: surface
- c: contour of a map
- n: various, like positions, lattice, tree, etc.
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.
- m: plain molecule built out of atoms
- p: polymer built out of atoms. These also carry additional
information about the monomers
- c: protein in C-alpha representation, (DNA, RNA for display
only): units are entire residues.
- f: pharmacophore
- k: force entry
- s: various special entries
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
- Go to '.../g/p' and specify the protein file '4dfr.pdb'
(a copy can be found in the directory 'moloc/dat' of the
download).
- A table with 8 items is displayed.
- Select 'whole list' which changes the specification number
of all items to '1'.
- Select 'MTX A' which changes the specification number of
this item to '2'.
- Select the 'x' item of the table. The program asks for
a color for all items '1', which are packed in a single
Moloc entry, and for a color for '4dfr_A_MTX' which is now a
separate Moloc entry.
- It is advisable to check the silent-H counts of the ligand
in 'dTp/h'. To do so the entry must be put into the active
state beforehand '.../a'!
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
- Go to '.../e' and select '4dfr_A_MTX'. This leads to a new
menu in which a Moloc entry can be handled.
- The three menu-items 'm', 'j', and 'o' (just before the
delete button 'd') allow to modify monomer information.
- Select 'o' (remove monomer information) which causes the
three monomer options to disappear. The entry is now a simple
molecule (m) and not a polymer (p) (see above).
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.
- To add the modified ligand entry to the rest-entry go to
menu item 'dTp/l'.
- Pick the ligand first, the rest-entry second. The program
then asks to provide monomer information:
- Monomer code (e.g. MOD).
- Chain id (A)
- Sequence number (not needed for heterogens)
- Insertion code (not needed for heterogens)
- Store united entry (previous rest-entry) as .pdb file
in '.../s/p'.