Tips and Tricks in Crystallography - Structure Analysis
Pavel Afonine: "phenix.fetch_pdb 1akg --maps" will fetch structure and
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.
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.
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
This site is maintained by Dr. Xinhua Ji (firstname.lastname@example.org) on the NCI-CCR-MCL server (http://mcl1.ncifcrf.gov).