usage:
entry-ribbons [-s] entry.pdb [nametag]
The default `nametag' is `entry'
The `-s' options splits the PDB file only, no ribbons data.
pdb-model
Create the required
*.model file.
pdbext-model
usage:
pdb-model molecule.pdb [name.model]
pdbext-model molecule.pdb [name.model]
The "molecule" and "name" above are the same string in the default cases. A model must have a name and a center for optional viewing. The center is taken as the average of the coordinates in the first case, and the center of the extremities in the second case. The name in this case is `name'. The file can be edited to change what appears on the menu or the initial center.
usage:
The first case creates a ribbon model only for the monomeric
protein `molecule.pdb'.
The second case creates a ball and stick model only from the input.
They can be used repeatedly to add additional molecules to the model,
eg:
atom-model mol2.pdb ModelName
usage:
Examples:
Note: When running interactively, CTRL-D gives an EOF signal.
usage:
ribbon-model
Create all the required files to run ribbons
for simple cases.
atom-model
atom-model molecule.pdb [name.model]
ribbon-model molecule.pdb [name.model]
pdb-sele-pdb
Select a subset of a *.pdb file based on a subset
X-PLOR `selection' syntax.
Most commands should work, except for wildcards.
Here you must have the 'sele = ( SelectionExpression )' format.
You should use either all upper- or lowercase for keywords,
and only certain abbreviations are allowed.
The keywords are: and, or, not, all, name, resi|resid|residue,
resn|resname, chem, hydr|hydro|hydrogen, point, cut, byres, around,
segi|segid, sele|select|selection.
If a floating point number is expected, the decimal must be present.
Also, the PDB `Chain ID' may be used as the X-PLOR `SEGId'
pdb-sele-pdb old.pdb new.pdb < sele.inp
sele = ( name ca ) --> pick only Calpha
sele = ( resi 10:30 ) --> range of residues
sele = ( name ca and resi 10:30 ) --> CAs in range
sele = ( chem o ) --> all oxygen atoms
sele = ( resname phe ) --> all phenyalanines
sele = ( resn phe or resid 1 ) --> all PHEs, plus res.1
sele = ( not hydro ) --> all but hydrogens
select = ( segid A ) --> all of chain A
select = ( point (31.2 27.3 4.2) cut 5.0 ) --> atoms near point
selection = ( byres resi 1 around 5.0 ) --> residues near res.1
pdb-geom-pdb
Create a Calpha *.pdb file based on the fit
of a run of residues to a helix
(see pdb-geom-ss ).
Suggested use is for tube and cylinder pictures.
The helix portion will roughly pass along the helix axis when
this *.pdb file is displayed as a ribbon with the
HelixShift parameter set to 0.0.
pdb-geom-pdb old.pdb new.pdb < pdb-geom-ss.output