Tips and Tricks in Crystallography - Structure Analysis

Pavel Afonine: "phenix.fetch_pdb 1akg --maps" will fetch structure and 
reflection data files from PDB and generate 2mFo-DFc and mFo-DFc maps (as well
as anomalous difference map if refection data is anomalous).

University of Cambridge, Department of Biochemistry: PyMOL tips and tricks

Visualization
Visualization of multiple alignments, phylogenies and gene family evolution
Visualization of macromolecular structures

Structure-based Multiple Sequence Alignment Programs: MUSTANG, MATT

Dr. Alla Gustchina (NCI): I'd like to share the link to a very useful website with examples of making publication quality figures by using PyMol, which I learned from my friend. I hope that link will be helpful to anybody if needed.
http://137.189.50.96/kbwong/teaching/pymol/pymol_tutorial.html

Mr. Jerry Alexandratos (NCI): KiNG. The Richardson lab has a new version of Kinemage, called KiNG. They're also putting out some new or improved programs: Backrub, for adjusting protein backbones; Probe, for viewing van der Waals, hydrogen bonding, and clashes; and MolProbity, for on-line checking your structures in progress. Rumors have it that they are working on a rotamer library for O and XtalView. Laura Murray of the Richardson lab are working on an RNA conformation library to help fix clashes in the sugar backbone. If we are lucky, this might be extended to a DNA rotamer library as well.

Dr. Lothar Esser (NCI): Now that your structure is solved, have you ever wondered if you have an antiparallel classic wide beta-bulge or whether that loop is in fact a type VIII beta turn ? Well I have and so I dug through the literature to find out the definitions of turns and bulges. It is a tedious exercise with the potential of getting it wrong. But there is help: PROMOTIF. Promotif is a program that reads a pdb file and produces postscript output with tables and graphics that describes the secondary structure elements: Secondary structure (more than DSSP), beta and gamma turns, disulfide bridges, beta bulges, beta hairpins, beta-alpha-beta units and psi-loops. In addition to defining residues as being strands or helices, it computes interacting helices. The postscript output of this program is really stunning and very informative. It is also able to compare multiple structures including NMR ensembles. 

Use: promotif "mystructure.pdb"
Example: promotif 3dni.pdb
Output: use a postscript viewer to look at numerous .ps files.
Author: E.G.Hutchinson and J.M. Thornton.
Fee: free for non-profits.
Source: Fortran code. You need to compile it. Works well on SGI (IRIX). g77 on Linux PCs gave problems. Most of them were easily solved. However some compilation problems could only be removed by drastic means: may result in incorrect output. 
pgf77 on biowulf had no problems after the switches -C -u from makefile2 were removed. (-C -u are not critical, useful for debugging) 
Ref.: E.G.Hutchinson and J.M. Thornton Protein Science(1996),5:212-220
URL: http://www.biochem.ucl.ac.uk/bsm/promotif/promotif.html