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Menu 'File'
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Menu 'File' is intendent for loading/saving files into/from Friend,
and saving current view as pictures in different formats.
Submenu 'Load' is intendent to load files into Friend.
- 'File->Load->Structure from files'
will pop up a file-chooser where a user can choose a file to load into
Friend. File should be in PDB fomat.
- 'File->Load->Structure from PDB'
will pop up a window where one can enter a PDB code
of structure to load or choose a structure from the PDB-codes list.
The actual loading is performed after ther user presses 'Fetch
structure' button. Friend will try to find the file .pdb, .ent,
where pdb-code is actuall PDB-code entered by user.
Friend looks for the file in the following way:
-- tries to load file from current directory and if fail;
-- tries to load file from the load PDB directory and if fail;
-- tries to load a files from the cache directory and if fail;
-- download structure from the PDB-web site, save it into cache
directory and load into Friend.
- 'File->Load->Alignment from file'
will pop up a file-chooser where a user can choose a file to load
into Firend. File should be in 'FASTA', 'PIR', 'CLUSTALW', 'CE', or
'SKY' format. The format of data is recognized by file extension:
for 'FASTA' format -- .fa .fst .fasta
for 'PIR' format -- .pir .ali
for 'CLUSTALW' format -- .aln
for 'CE' format -- .cea
for 'SKY' format -- .sky
- 'File->Load->Alignment from text box'
will pop up a window allowing a user to load an aligment as
text. The window contains the text box, where the actuall alignment
must be paste, and fomat specification chooser.Alignment should be in
'FASTA', 'PIR', 'CLUSTALW', 'CE', or 'SKY' format.
Submenu 'Save' is intendent to save data loaded in Friend into files.
- 'File->Save->Structure to file'
will pop up a file chooser where one can choose a file to save
structure currently loaded to Friend. Only structure data will be
save in the PDB format.
- 'File->Save->Alignment to file'
will pop up a window allowing a user to save currenly
loaded into Friend alignemt to a file. One have to choose a file and
specify the format of data saving. Format can be in 'FASTA', 'PIR',
'CLUSTALW', 'CE', or 'SKY'.
Submenu 'Export' is intendent to save current view in Friend as a picture
in different graphical formats.
- 'File->Export->Structure view as PNG'
save the current view of structures in PNG file.
- 'File->Export->Structure view as JPEG
save the current view of structures in JPEG file.
- 'File->Export->Structure view as postscript'
save the current view of structures in PostScript file.
- 'File->Export->Alignment view as postscript'
save the current view of sequence alignment in PostScript file.
- 'File->Copy'
copies current view of structures to the clipboard. Currently this
function is implemented only on Windows platform.
- 'File->Close all'
unload all structures and sequences from Freind and clear
strucure and sequence window.
- 'File->Exit'
exit Friend.
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Menu 'Edit'
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Menu 'Edit' contains menu items intended to organize work
with sequences in the 'Sequence Alignmnet Window'.
- 'Edit->Groups'
selectes of this Item brings Group-editor dialog. Group-editor Dialog
lets to create/edit groups of sequences;
- 'Edit->Remove gapped columns'
removes columns which are gapped for all sequences on alignment;
- 'Edit->Remove redundancy'
removes redundant sequences based on string representation of the
sequence;
- 'Edit->Remove ID redundancy'
removes redundant sequences based on sequences' IDs.
- 'Edit->Remove selected sequences'
removes selected sequences from alignmnet alogn with corresponding
structures.
- 'Edit->Select all sequences'
selects all sequences;
- 'Edit->Deselect all sequences
deselects all sequences;
- 'Edit->Invert sequence selection'
invertes seqeucen selection;
- 'Edit->Scores'
shows additional annotation field field for residues in the alignment.
- 'Edit->Group editing mode'
turns on/off the editing of the sequence groups.
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Menu 'Sort'
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Menu 'Sort' contains menu items intended to sequence in the alignment.
- 'Sort->By group'
sorts all sequences based on group;
- 'Sort->By length'
sorts all sequences based on sequence-length;
- 'Sort->By ID'
sorts all sequences based on ID;
- 'Sort->By organism'
sorts all sequences based on organism;
- 'Sort->By tree order'
sorts all the sequences by the order as they appear in the tree (a tree
must be produced to use this command);
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Menu 'Display'
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Menu 'Display' is intendent to change the representation of molecules
on the screen. Commands in this menu act only on selected atoms.
- 'Display->Wireframe'
show covalent bonds as thin wires, do not show atoms;
- 'Display->Backbone trace'
show peptide bond as thick wires, do not show the rest;
- 'Display->Trace'
show peptide bond as thick wires with smoothen contact angles, do
not show the rest;
- 'Display->Sticks'
show bonds bonds thick wires, show atoms as small balls;
- 'Display->Spacefill'
show atoms as Van der Waals radii, do not show the rest;
- 'Display->Ball & stick'
show bonds bonds thin wires, show atoms as small balls;
- 'Display->Ribbons'
show a ribbon alogn the peptide bond; do not show the rest;
- 'Display->Strands'
show strands along the peptide bond; do not show the rest;
- 'Display->Cartoons'
show a ribbon alogn the peptide bond, make it thicker where secondary
structure is present, do not show the rest;
- 'Display->HBonds'
show hydrogen bonds;
- 'Display->TBonds'
show bonds of Delaunay tesselation;
- 'Display->SSBonds'
show disulphide bridges.
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Menu 'Colors'
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Menu 'Colors' is intendent to change the color of structures and
sequences. Commands in this menu can act on selected atoms/residues as
well as on all atoms/residues.
- 'Colors->Structure'
color molecules by secondary structure;
- 'Colors->Alignment'
colors alignment and not aligned part (as shown in 'Sequence Alignment
Window') by different colors;
- 'Colors->Molecule'
color each molecule by different color;
- 'Colors->Chain'
color each chain by different color;
- 'Colors->Residue type'
color each residue type by different color;
- 'Colors->Monochrome'
color all atoms by grey;
- 'Colors->CPK'
color each chemical atom type by different color;
- 'Colors->Start-to-end'
color each chain from N-terminal to C-terminal with gradualy chainging
color;
- 'Colors->Temperature'
color molecules by temperature factory;
- 'Colors->Model'
color each model (of NMR structures) by different color;
- 'Colors->Clustalx'
color sequences by alignment using ClustalX color scheme.
Submenu 'On properties' allows to color all residues for marked sequences.
- 'Colors->On properties->Zappo'
color residues by similarity in chemical properties;
- 'Colors->On properties->Taylor'
color residues by similarity in chemical properties;
- 'Colors->On properties->Hydrophobicity'
color residues by their hydrophobicity;
- 'Colors->On properties->Helix propensity'
color residues by their helix propensity;
- 'Colors->On properties->Strand propensity'
color residues by their strand propensity;
- 'Colors->On properties->Turn propensity'
color residues by their turn propensity;
- 'Colors->On properties->Buried index'
color residues by buried index.
Submenu 'Choose' allows to choose color.
- 'Colors->Choose->Atoms'
choose color for atoms;
- 'Colors->Choose->Background'
choose color for backbround;
- 'Colors->Choose->HBonds'
choose color for hydrogen bonds;
- 'Colors->Choose->TBonds'
choose color for t-bonds;
- 'Colors->Choose->SSBonds'
choose color for disulphide bridges.
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Menu 'Select'
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Menu 'Select' is intendent to select specific group of atoms to futher
applay actions (change color or representation) to them. It is used
together with the logic selection handeled by drop-down choice in
the toolbar. The action of the commands in this menu are extended on
all the molecule currently in the memory.
- 'Select->All'
select all atoms;
- 'Select->Invert'
invert previous selection, e.g. unselect selected atoms and
select not selected atoms;
- 'Select->Aligned'
select atom which were previously aligned by commands
Align->'Fit by alignment' or
Align->'Align->Fit by TOPOFIT'
(see menu 'Align' for details);
- 'Select->Residue->...'
select all atom in named residues;
- 'Select->Atom->...'
select specific atom in all residues;
- 'Select->Hydrogens'
select all hydrogens;
- 'Select->Not hydrogens'
select all hydrogens excluding hydrogens;
Submenu 'Hetero' is intendent to select atoms not constituing proteins
and DNAs.
- 'Select->Hetero->Hetero'
select all the hetero atoms;
- 'Select->Hetero->Solvent'
select all the solvent hetero atoms;
- 'Select->Hetero->Non solvent'
select all the non solvent hetero atoms;
- 'Select->Hetero->Water'
select atoms constituting water molecules;
- 'Select->Hetero->Ions'
select ions;
- 'Select->Hetero->Ligands'
select atoms constituing ligands;
Submenu 'Protein' is intendent to select atom forming proteins. The
selection can be made on the basis of physico-chemical properties of
residues, their size, location in a protein and constituing structure
(alpha helix, beta strand, turn, loop or backbone).
- 'Select->Protein->Protein'
select atom constituing proteins;
- 'Select->Protein->Amino'
select atoms constituing amino acid residues;
- 'Select->Protein->Large'
select large size residues;
- 'Select->Protein->Medium'
select medium size residues;
- 'Select->Protein->Small'
select small size residues;
- 'Select->Protein->Alpha carbons'
select alpha carbons of residues;
- 'Select->Protein->Backbone'
select atoms forming backbone;
- 'Select->Protein->Bonded'
select covalently linked atoms;
- 'Select->Protein->Buried'
select atoms in buried residues;
- 'Select->Protein->Helix'
select all atoms in residues forming alpha helices;
- 'Select->Protein->Sheet'
select all atoms in residues forming beta sheets;
- 'Select->Protein->Sidechain'
select atoms constituing sidechains of all residues;
- 'Select->Protein->Surface'
select all atoms in residues exposed on the surface;
- 'Select->Protein->Turn'
select all atoms in residues forming turns;
- 'Select->Protein->Acidic'
select all atom in acidic residues;
- 'Select->Protein->Acyclic'
select all atoms in acyclic residues;
- 'Select->Protein->Aliphatic'
select all atoms in aliphatic residues;
- 'Select->Protein->Aromatic'
select all atoms in aromatic residues;
- 'Select->Protein->Basic'
select all atoms in basic residues;
- 'Select->Protein->Charged'
select all atoms in charged residues;
- 'Select->Protein->Cyclic'
select all atoms in cyclic residues;
- 'Select->Protein->Cysteine'
select all atoms in cysteins;
- 'Select->Protein->Hydrophobic'
select all atoms in hydrophobic residues;
- 'Select->Protein->Neutral'
select all atoms in neutral residues;
- 'Select->Protein->Polar'
select all atoms in polar residues.
Submenu 'Nucleic' is intendent to select atom forming DNAs and RNAs.
- 'Select->Nucleic->Nucleic'
select all atoms constituing DNAs and RNAs;
- 'Select->Nucleic->DNA'
select all atoms constituing DNAs;
- 'Select->Nucleic->Backbone'
select all atoms constituing sugar backbone;
- 'Select->Nucleic->AT'
select all atoms in adenosine and threonine;
- 'Select->Nucleic->GC'
select all atoms in guanine and cytosine;
- 'Select->Nucleic->Purine'
select all atoms in purine bases;
- 'Select->Nucleic->Pyrimidine'
select all atoms in pyrimidine bases.
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Menu 'Options'
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Menu 'Options' provides a user with options for visualization.
- 'Options->Stereo'
turns on/off the stereo view of structures;
- 'Options->Hetero atoms'
hide/show hetero atom;
- 'Options->Labels'
show hide labels on atoms (acts only on selected atoms);
- 'Options->Specular'
turns on/off spectacular drawing (doesn't change the representation,
changes only the way of drawing);
Submenu 'Sequence window' is intendent ot change the placement of the
sequence window.
- 'Options->Sequence window->Left'
put the sequence window at the left side of the main window;
- 'Options->Sequence window->Right'
put the sequence window at the right side of the main window;
- 'Options->Sequence window->Bottom'
put the sequence window at the bottom of the main window;
- 'Options->View options'
brings a new window where viewin options can be changed.
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Menu 'Calculate'
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Menu 'Calculate' is intendent for analysis of the requiring
calculations.
- 'Calculate->Average distance tree
using PID'
calculates average distance tree using per cent of sequence
identity in the alignment editor as distance;
- 'Calculate->Neighbor joining tree
using PID'
calculates neighbor joining tree using per cent identiry between
sequences in the current alignment as distance;
- 'Calculate->NJT using pair alignment'
calculates the neighbor joining tree using per cent identity between
sequences in pairwise alignment as distance;
- 'Calculate->Principal component
analysis'
brings a new window to perform principal component analysis of the
sequences in current alignment;
- 'Calculate->Consensus'
calculate and display the consensus of the current alignment;
- 'Calculate->Conservation'
find conserved positions in the alignment;
- 'Calculate->Hydrogen positions'
calculates hydrogen postions on structures loaded;
- 'Calculate->Hydrogen bonds'
calculates hydrogen bonds in structures loaded.
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Menu 'Align'
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Menu 'Align' collects commands to perform various kinds of alignments.
- 'Align->Pairwise'
makes pairwise alignment of the two marked sequences;
- 'Align->Pairwise PID'
calculates and prints per cent identity of the current alignment for two
marked sequences;
- 'Align->Fit by alignment'
superimposes structures based on the current alignment, i.e. minimize
RMSD between CA atoms of the aligned residues;
- 'Align->By TOPOFIT'
alignes structures for two marked sequences using TOPOFIT method.
Brings a new frame where default parameters used in the method can be
changed;
- 'Align->By TOPOFIT'
alignes structures for two marked sequences using TOPOFIT method with
default parameters;
- 'Align->ClustalW'
makes multiple sequence alignment using ClustalW (you have to intall
ClustalW and configure Friend properly in advance);
- 'Align->Mucec'
alignes structures for two marked sequences using CE method
(you have to intall CE and configure Friend properly in advance).
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Menu 'Visible'
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Menu 'Visible' allows to hide/show particular structure loaded in the
Friend.
- 'Visible->All'
shows all structures loaded;
- 'Visible->Aligned chains only'
shows only loaded structures corresponding to the chains in the alignment
editor;
- 'Visible->Marked chains only'
shows only loaded structure corresponding to the marked chains;
- 'Visible->Hide all'
hides all structures loaded;
- 'Visible->Hide marked chains only'
hides loaded structures corresponding to the marked chains.
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Menu 'Help'
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Menu 'Help' provides access to the general information about the programg
and to user manual.
- 'Help->Manual'
brings a new frame with Friend manual;
- 'Help->About'
brings a new frame with general information about Friend.
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