Next: selection from an expression Up: Subset selection Previous: selection from a selection Contents

#### selection from the loaded trajectory

To perform a subset selection from the loaded trajectory, you have to click on the from the loaded trajectory radiobutton. A dialog will be displayed in the underneath frame from which you will construct your selection directly from the contents of the universe related to the loaded trajectory (see Fig. 4.22).

Figure 4.22: The subset selection dialog for a selection from the loaded trajectory.

To construct the selection, it is compulsory to proceed in the following order:

1. select an object name among the ones displayed in the Object name listbox. This will display in the Selection keywords listbox the selection keywords associated to the selected object.
2. select a selection keyword among the ones displayed in Selection keywords listbox. This will display in the Selection value listbox the values associated to the selected keyword.
3. unselect/select one or several values among the ones displayed in the Selection value listbox.

By doing so, you will construct a selection string with the following format:
objectname name keyword value1,value2, ...
where name is the selected object name (step 1), keyword is the selected keyword (step 2) and value1,value2,... are the selected values (step 3). This constructed selection string, that will be used by nMOLDYN, is displayed in the Selection preview entry at the bottom of the dialog with highlighted keywords.

You can associate several selection keywords to a given selected object by repeating steps 2,3. In that case, the constructed selection string will have the following format:
objectname name keyword1 value1,value2,...OR keyword2, value1,value2,value3...
where the keyword OR will be interpreted by nMOLDYN as an union operator in the sense that it will take the union between the set of atoms generated by keyword1 value1,value2, keyword2 value1,value2,value3 ...

You can also include several objects in the selection by repeating steps 1,2,3. In that case, the constructed selection string will have the following format:
objectname name1 keyword1 value1,...OR keyword2, value1,value2, ...OR objectname name2 keyword1 value1 ...
Finally, using the buttons within the Linkers frame each time a step 3 is completed allows to construct more complex selection strings using the (, ), AND, OR linkers, the AND linker acting as an intersection operator while the OR link, described above, acts as an union operator. The button Clear clears up the selection string under construction.

The table 4.1 lists the selection keywords and values depending on the MMTK type of the object being processed.

Table 4.1: List of selection keywords and their associated values according to the MMTK type of the selected object.
Object MMTK type | Selection keyword | Selection value
Atom | name | the object MMTK name
AtomCluster | atomelement | the element name (e.g. hydrogen)
| atomname | the atom MMTK name
| name | the object MMTK name
Molecule | chemfrag | the chemical fragment name. One of amine, hydroxy, methyl or thiol
| atomelement | the element name (e.g. hydrogen)
| atomname | the atom MMTK name
NucleotideChain | atomelement | the element name (e.g. hydrogen)
| atomname | the atom MMTK name
| atomtype | the atom MMTK type
| misc | one of backbone or bases
| name | the object MMTK name
| nuclname | the nucleotide MMTK name.
| nucltype | the nucleotide MMTK type
PeptideChain | chemfrag | the chemical fragment name. One of amine, c_alphas, hydroxy, methyl or thiol
| atomelement | the element name (e.g. hydrogen)
| atomname | the atom MMTK name
| atomtype | the atom MMTK type
| misc | one of backbone or sidechains
| name | the object MMTK name
| resclass | the residue class. One of acidic, aliphatic, aromatic, basic, charged, hydrophobic, polar or small
| resname | the residue MMTK name
| restype | the residue MMTK type
Protein | chemfrag | one of amine, c_alphas, hydroxy, methyl or thiol
| atomelement | the element name (e.g. hydrogen)
| atomname | the atom MMTK name
| atomtype | the atom MMTK type
| chainname | the chain MMTK name
| misc | one of backbone or sidechains
| name | the object MMTK name
| resclass | the residue class. One of acidic, aliphatic, aromatic, basic, charged, hydrophobic, polar or small
| resname | the residue MMTK name
| restype | the residue MMTK type

Here are some examples of subset selection strings constructed from a protein whose name is P892:

- objectname P892 atomelement carbon: will select only the carbon atoms,
- objectname P892 atomelement carbon,hydrogen: will select only the carbon and hydrogen atoms,
- objectname P892 atomelement oxygen and restype Ala,Arg: will select only the oxygen atoms of Alanine and Arginine residues,
- objectname P892 atomelement carbon OR resclass acidic: will select all the carbon atoms plus the all the atoms of the acidic residues.

Next: selection from an expression Up: Subset selection Previous: selection from a selection Contents