Bioinformatics

Modeling with PyMOL

Saving with transformed coordinates

Translate or rotate individual objects

There is a "translate" function similar to "rotate", the docs for these don't exist yet, because the implementation isn't finished. However, feel free to use them in the following forms:

translate vector,object-name,state
   (vector needs to be something like [x,y,z])

   translate [1,0,0],pept

rotate axis,angle,object-name,state
   (axis can be either the letter x,y,z or a 3D vector [x,y,z])

   rotate x,90,pept
   rotate [1,1,1],10,pept

Moving one segment relative to the rest

Split states to objects

There is also a new command in the 0.95 series:

   split_states object-name

Altering secondary structures:

Examples:

 alter A/10:34/, ss='H'
 alter A/35:40/, ss='L'
 alter A/41:60/, ss='S'

Altering van der Waals radii

Example:

alter (elem Fe),vdw=1.8
rebuild

Altering atom coordinates

Example:

alter_state 1,(pdb1cse),x=x-10.0 

Deleting bonds

Select the bond using Ctrl-right-click, then either

unbond pk1,pk2

Converting D- to L- amino acids

The inversion function was changed in version 0.95 to take advantage of multiple picked atoms. To invert a center, Ctrl-middle-click to pick the center atom as pk1 and two stationary atoms as pk2 and pk3. Then type Ctrl-E to invert.

Adding disulfide bonds

You can use the "bond" command to attach them:

bond 24/sg,26/sg
bond 56/sg,99/sg

unpick

alter cys/,name='CYX'

alter 24+26+56+99/,name='CYX'

Adding hydrogen bonds

Regarding H-bonds. There isn't a built-in function yet, but you can show H-bonds between two objects using atom selections so long as hydrogens are present in both molecules. If you don't have hydrogens, you can use h_add on the proteins or provide ligands with valence information and then use h_add.

Two examples are below. For clarity, they draw dashes between the heavy atoms and hide the hydrogens.

Protonating ligands

If your ligands come in with valid valencies and formal charges, PyMOL's h_add command can protonate ligands. (NOTE that there is a minor technical hiccup with SD-files which are loaded by default as immutable "discrete" objects.) Suffice it to say that in order to make changes to the chemical structure, an object must be loaded with the "discrete" flag set to zero.
Unfortunately, much of the molecular editing stuff remains to be documented. Here's an example sequence, but I'm not sure it will help to much...as indicated in the manual, this is immature functionality with some major gaps. Attach in particular is very limited...

# show valences
set valence=0.05

# load cysteine fragment
fragment cys

# remove hydrogens
remove (hydro)

# edit gamma S
edit cys////sg

# add hydrogen
attach H,1,1

# add planer, trivalent nitrogen onto C terminus
edit cys////C
attach N,3,3

# edit that nitrogen
edit (elem N and neighbor cys////C)

# attach a tetrahedral methyl (note random position)
attach C,4,4

# here's an example of adding a whole residue from the library
edit cys////N
editor.attach_amino_acid("pk1","ace")

# now restore missing hydrogens (note that the names are off...)
h_add

Superposition of two molecules

Using pair_fit requires that you specify a set of paired atoms in each structure. Fortunately, you no longer have to specify each pair separately, so long as the ordering is the same in each selection (almost always true).

pair_fit ( trna10 and resid 10:15 and name P ), ( ref4 and resid 10:15 and
name P )

pair_fit prot1///11-26/CA, prot2///34-49/CA