Set up
Set working directory |
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Load pdb file from pdb website |
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Load pdb file from local disk |
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Log files
new log file |
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save and quit log file |
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comment |
# |
record the view coordinate |
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run a log as a script |
`@file_name.pml |
resume log file = run then edit at the end
append log file = edit at the end without running
Selection
select selection_name, selection_expression |
select carbon_beta, n. cb
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select selection_name= (selection expression) |
select carbon_beta = (n; cb)
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logical operator: and (/), not, or. !order of precedence --> use ()
Selection - single word
All atoms |
all |
* |
No atoms |
none |
none |
All hydrogen atoms |
hydro |
h. |
All atoms from HETATM record |
het |
hetatm |
Porperty selector identifiers
Atom by chemical symbol
ex: Oxygen = O |
symbol |
e. |
Atom/nucleic acid by code
ex: Cα = ca, Cβ = cb |
name |
n |
Aa/nucleic acid by code
ex: Asparagine = asp / adenosine = a |
resn |
r |
residue identifier (1-9999) |
resi |
i |
PDB chain identifier (check in PDB file if letter or number ID) |
chain |
c |
Secondary structure:
α helix = 'H', β strand = "S", Loop = 'L' |
ss |
ss |
carbon α : first carbon bond to the side chain
carbon β : second carbon bond to the side chain
selection macros
/object−name/segi−identifier/chain−identifier/resi−identifier/name−identifier |
start by "/": start from the top of the hierarchie (object-name) |
end by "/": start from the bottom of the hierarchie (name-id) |
// :skip one level of hierarchie |
ex: select lys, /helix_alpha///lys
select all the residue of lysine from the object "helix_alpha" |
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Diplay
show the selection as this diplay type |
show_as lines, selection_name
cmd.show_as("lines", "selection_name")
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add this display type of the selection |
show lines, selection_name
cmd.show("lines", "selection_name")
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hide this display type of the selection |
hide lines, selection_name
cmd.hide("lines", "selection_name")
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color the selection |
coloc color_name, selection_name
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zoom on the selection |
zoom selection_name |
Show (S button) - Hide (H button) - Color (C button)
display type: lines, ribbon, cartoon, stick, label, nonbonded, mainchain, sidechain
Structure modification
adds hydrogens in the appropriate places |
h_add |
get information
count the number of atome of the selection |
count_atoms selection_name
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selection algebra
Selects atoms that are not included in s1 |
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Selects atoms included in both s1 and s2 |
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Selects atoms included in either s1 or s2 |
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Selects atoms in s1 whose identifiers name, resi, resn, chain and segi all match atoms in s2 |
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Selects atoms in s1 whose identifiers name and resi match atoms in s2 |
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Selects all atoms whose van der Waals radii are separated from the van der Waals radii of s1 by a minimum of X Angstroms. |
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Selects atoms with centers within X Angstroms of the center of any atom in s1 |
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Expands s1 by all atoms within X Angstroms of the center of any atom in s1 |
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Selects atoms in s1 that are within X Angstroms of the s2 |
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Expands selection to complete residues |
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Expands selection to complete objects |
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Selects atoms directly bonded to s1 |
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