A collection of miscellaneous images accrued in the course of PyMOL work for myself and others...
FCC lattice Richard
Implementing a "sausage"-style cartoon ("putty") Warren
CGOs of sliced cubes
CGO-based cartoons of oligomeric proteins Vero
Chemical modification: breaking and making covalent bonds Loren
Display idealized (i.e., calculated) electron density for a diatomic molecule (Cl2) Anna Klein
Illustration of variable loop settings
Visualize electron density maps carved about a selection Loren
Test files for MacPyMOL scene switching John
Images of P. Tieleman's "m65" MD-equilibrated micelle Linda
Least-squares fitting of a plane to a set of atoms dave, jeff
Cartoon reps with variable transparency davidB
Counting & visualizing interatomic contacts jamie
Getting SuperSym to play nice with PyMOL and CCTBX mikey

FCC lattice_montage.png

Implementing a "sausage"-style cartoon ("putty")



Red, yellow, green, and blue balls:

Protein Vegas:

Extrusion points:


much closer...:

very near I:

very near II (fixed termini caps):
...flip about <y>...
very near III (smoothening via window averaging):
nosmooth1.s.png (no smoothing): averaging_asymmetric1.s.png (3-point window):
averaging_symmetric1.s.png (3-point window): averaging_symmetric2.s.png (5-point window):

finally, a real example (14-mer from 1M5Q 28-mer):

Symmetries of sliced CGO cubes:

CGO-based cartoons of oligomeric proteins:

It may be necessary to do geometric sorting of vertices if the default sequence of chain IDs does not conform to a convex polygonal cycle. For example, in the following images the chain IDs of the input PDB file were all set to 'D', so chain sequence information was effectively lost. The left panel illustrates the CGO that results if the vertices are not sorted, whereas the CGO in the right panel was created after sorting (see my makeCGOplates.py module).

Also, two-sided lighting may be important for successful ray-tracing of some CGOs (left=OFF; right=ON):

Chemical modification: Using PyMOL to break (and make) covalent bonds

The following is an image of the starting structure, built in PyMOL's default (β-sheet) geometry using the BuildResidueAla menu sequence:

The following image is of the broken structure, produced from the above object by (i) going into the Mouse → 3 Button Editing Mode, (ii) picking the bond of interest (near the center); (iii) using the Build → Remove [Ctrl-D] command. The two resultant fragments were then written-out to separate PDB files (using the molecule selection) -- bonding1_frag1.pdb and bonding1_frag2.pdb.

Finally, PyMOL was reinitialized, and the two PDB files above were loaded. A bond was created between the two fragments by using the "fuse" command with the two atoms as arguments – e.g., "fuse (frag1 and resi 5 and name C), (frag2 and resi 6 and name CA)". Note that PyMOL provides two methods for fusing atoms into bonds ("fuse" and "bond"), and that these two methods are not exactly equivalent in terms of requiring that the target atoms belong to the same PyMOL object – see the descriptions of the "bond" and "fuse" syntaxes in the PyMOL Reference Manual). Note also that the original fused selection (green carbons) is reoriented so as to better satisfy PyMOL's bond-geometry criteria (pink carbons).

NOTE: Another example:
Download a sample PDB file (union1.pdb) containing two atoms separated by more than the usual ~1.5-A bond distance. We will now force a bond between these two atoms via the following sequence of steps:
Display idealized (i.e., calculated) electron density for a diatomic molecule (Cl2):

This is included here in the sandbox section (for now) rather than the main PyMOL page because de novo calculation of ideal electron density for a molecule is outside the scope of PyMOL. Instead, this may be achieved using standard crystallographic software such as CCP4's SFALL and FFT. The following is a description of how I calculated and visualized the ideal electron density for diatomic chlorine. Note that by "ideal" I mean that actual (i.e., quantum-mechanically derived) atomic scattering factors were used for chlorine rather than structure factors which have been calculated from observed reflection intensities (which is what is generally done in a crystallographic experiment), atomic B-factors were set to 0.0, and the calculation was performed in the scattering range 500→5 Å. The explanation is excerpted from an email, and is followed by the files specified in the description:

> 2) How can I display both the atoms and the electron density in the SAME place.

This is a little more tricky. The easiest way to guarantee that it works -- especially for something relatively simple, like a diatomic molecule -- is to center the object in a cell, and then perform the map calculation over this structure. It seems like your original structure was not properly centered, or the map was calculated with respect to a different origin, or some problem of this sort (sorry, I didn't have time to carefully analyze it). I solved this problem by doing the following steps:

(1) I took your input PDB file and reformatted it to get the file "mycl2_b0.pdb" (attached to this email). The main things which I did were to clean-up the atom names, chain and segid syntax, set B-factors to 0.0, provide unit cell info. (required in the map calculation in next step), etc., and translate the diatomic molecule to the center of a 10.0-Angstrom cubic unit cell...

(2) Then I calculated an electron density map from this centered P1 structure using the CCP4 program SFALL (http://www.ccp4.ac.uk/dist/html/sfall.html -- see the attached file "sfall2.csh")...

(3) Then I visualized the resulting density and molecule using a PyMOL script file -- please see the attached file "mycl2.pml" and compare the commands against those in the user manual to understand exactly what's going on...

(4) Ray-tracing of the PyMOL view resulted in the final image file "mycl2_view1.png" (attached). Hopefully this is something along the lines of what you had in mind?

I haven't attached the CCP4-formatted map file because it is rather large (3.8M) for an email attachment.

With best regards,

Here is an image of the map and the relevant files:

mycl2_b0.pdb – PDB-format coordinates for the atomic structure in a triclinic unit cell, 10-Å/edge
sfall2.csh – CCP4 script used to calculate by FFT of atomic structure factors
mycl2.pml – PyMOL macro/script used to display and render a graphical image of the map

Illustration of variable loop settings:

1I8F_a.pdb – PDB-formatted coordinates for this example
1i8f_a_cartoons.pml – This example as a PyMOL macro

Visualize electron density maps carved about a selection:

mapExample4Loren.tar.gz – GNU zip'd tar archive containing all the files for this example ("tar zxvf mapExample4Loren.tar.gz" to unpack it).

Loren – this (below) is what you're talking about?

Test files for MacPyMOL scene switching:
  1. 1AZV.pml → PyMOL script file
  2. 1AZV.pdb → PDB file for the test protein
  3. 1AZV_scene7.png → Ray-traced illustration of Scene 7 (shown below)
  4. macpymol-0_99rc6.tar.gz → The actual MacPyMOL which was cleanly installed and used for these tests
Ray-traced illustration of Scene 7:

Micelle images:
(click on thumbnails for larger versions)

Fitting planes to atoms:
(click on thumbnails for larger versions)

Cartoon representations with variable transparency levels:
(click on images for larger versions)

Counting a set of interatomic contacts and visualizing the result:
(click on thumbnails for larger versions; note that panels A→C are in VMD)
(A) within the entity: (B) between the entity and its neighbors: (C) zoomed-in view of (b):
(D) number density of contacts via scaled putty:

Getting PyMOL to play nice with CCTBX and the 'SuperSym' module:
(click on images for larger versions)