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PyMOL>load dat/il2.pdb
CmdLoad: "dat/il2.pdb" loaded as "il2".
PyMOL>load dat/pept.pdb
CmdLoad: "dat/pept.pdb" loaded as "pept".
PyMOL>load dat/3al1.pdb
HEADER STRUCTURAL PROTEIN 26-OCT-98 3AL1
TITLE DESIGNED PEPTIDE ALPHA-1, RACEMIC P1BAR FORM
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: D, L-ALPHA-1;
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES;
COMPND 5 OTHER_DETAILS: N TERMINI ARE ACETYLATED
ObjectMolecule: Read secondary structure assignments.
ObjectMolecule: Read crystal symmetry information.
Symmetry: Found 2 symmetry operators.
CmdLoad: "dat/3al1.pdb" loaded as "3al1".
PyMOL>util.ss
util.ss: WARNING: This is not a "correct" secondary structure
util.ss: assignment algorithm! Please use only as a last resort.
util.ss: initiating secondary structure assignment on 163 residues.
util.ss: extracting sequence and relationships...
util.ss: analyzing phi/psi angles (slow)...
util.ss: finding hydrogen bonds...
util.ss: verifying beta sheets...
util.ss: assignment complete.
PyMOL>util.cbac
Executive: Colored 1948 atoms.
Executive: Colored 922 atoms.
PyMOL>util.cbay
Executive: Colored 1948 atoms.
Executive: Colored 922 atoms.
PyMOL>util.cbaw
Executive: Colored 1948 atoms.
Executive: Colored 922 atoms.
PyMOL>util.cbas
Executive: Colored 1948 atoms.
Executive: Colored 922 atoms.
PyMOL>util.cbc
util.cbc: color 26,(chain A)
Executive: Colored 279 atoms.
util.cbc: color 5,(chain B)
Executive: Colored 310 atoms.
util.cbc: color 154,(chain E)
Executive: Colored 107 atoms.
util.cbc: color 6,(chain '')
Executive: Colored 2174 atoms.
PyMOL>hide
PyMOL>show car
PyMOL>zoom
PyMOL>set ray_default_renderer=2
Setting: ray_default_renderer set to 2.
PyMOL>ray
RayRenderTest: obtained 19492 graphics primitives.
PyMOL>util.rainbow("pept")
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