Bond Cylinder Data Preparation

pdb-bond --- make bond *.cyl file
sph-bond --- make split bonds colored by sphere type
pdb-link-ca --- make C-alpha trace
sph-link --- make bonds by linking successive spheres
pdb-bf-bond --- make bond *.cyl file, color by B-factor
pdb-hb-cyl --- output mainchain H-bonds in *.cyl format
ms-cyl --- converts *.dot file to *.cyl file
pdb-hx-fit --- fit ranges of alpha carbons to ideal helices
fithelix --- fit alpha carbons to helices
bestfits --- best-fits helices to a range of C-alphas
interhx --- calculates angles between helices
hx-mono-cyl --- convert pdb-hx-fit output to mono-color cylinders
hx-dipole-cyl --- convert pdb-hx-fit output to multi-color cylinders

Generally programs run with interactive input, producing a small amount of diagnostic output. Preparation of bonds is based on the assumption of near ideal geometry and only the `biological' elements H,C,N,O,S, and P. The simple format of the *.cyl file allows one to easily reformat some special `bond' list for use with the program.

The programs all have the following general usage features:

usage:
xxx-bond [options] mol.xxx mol.cyl [> diagnostics]

  options:
    -r radius  -- set all radii to `radius' (float).
    -k N       --  set all bonds to color `N' (int).

errors:
*.pdb file does not exist.
*.sph file already exists.

pdb-bond

Create cylinders from atomic bonds implied by the *.pdb coordinates. Defaults bond radius is 0.15 and default color is 7 (white).

usage:
pdb-bond molecule.pdb molecule.cyl

sph-bond

Create "split-bonds" based on the color assigned to the spheres. Defaults bonds radius is 0.15 angstroms.

usage:
sph-bond molecule.sph molecule.cyl

pdb-link-ca

Create a C-alpha tracing with linked cylinders and spheres.

usage:
pdb-link-ca mol.pdb mol_ca.sph mol_ca.cyl

Note: Defaults to carbon atom radius, colored green (2), bonds with radius = 0.15 angstroms. No options, change interactively.

sph-link

Create a linked set of cylinders colored according to spheres.

usage:
sph-link mol_ca.sph mol_ca.cyl

Note: Defaults to bonds with radius = 0.15 angstroms. No options, change interactively.

pdb-bf-bond

Create "split-bonds" based on the B-factors of the atom. Defaults bonds radius is 0.15 angstroms.

usage:
pdb-bbond molecule.pdb molecule.cyl

Note: Default B-factor scale and colors correspond to my sensibilities. The mapping of the ranges of B to a colorindex are set with a file like $RIBBONS_HOME/data/bf.colors. To change, use option:
-c bf.colors_file .

pdb-hb-cyl

Output the mainchain hydrogen bonds in *.cyl format. The default radius is 0.10 angstroms.

usage:
pdb-hb-cyl file.pdb file.cyl

ms-cyl

ms-cyl MS dots to 'circles' Convert a *.dot file into very short cylinders (or set a specific length with `-l' option) aligned with the dot's normal. Produces shaded disks of variable radius.

usage:
ms-cyl [-l length] file.dot file.cyl

pdb-hx-fit
hx-dipole-cyl
hx-mono-cyl

Fit the alpha carbons of the *.pdb file for each of the residue ranges to an ideal helix. These range files may be made with ss-hx-range . Convert the fit output to cylinders, either `mono' for a single cylinder per helix, or `dipole' for 3 cylinders per helix that color the dipole direction.

usage:
pdb-hx-fit mol.pdb mol_helix.range > mol_helix.fit
hx-mono-cyl mol_helix.fit mol_helix.cyl
hx-dipole-cyl mol_helix.fit mol_helix.cyl

See the Calmodulin example .

fithelix

Used by pdb-hx-fit .

See $RIBBONS_HOME/fithelix/ for scripts and examples.

bestfits
interhx

bestfits mol_helix.range < protein.pdb > bestfits.out
interhx < bestfits.out > interhx.out

See $RIBBONS_HOME/fithelix/ for scripts and examples.

Ribbons User Manual / UAB-CMC / carson@cmc.uab.edu