CNS

CNS stands for "Crystallography and NMR System" and is an integrated and full-featured program for the determination and refinement of X-ray crystallographic and NMR structures.

Among its capabilities is simulated annealing molecular dynamics refinement.

• CNS home page and wiki

There is a parallelization (OpenMP) source code patch for CNS from Kay dot Diederichs at uni-konstanz dot de. It is now distributed with CNS 1.2 as an alternate download. The parallel version features (roughly) a 2-fold speedup on a 4-core machine for a typical simulated annealing omit map run.

Joe Krahn is working an RPM spec for installing CNS on Linux, which includes standard and OpenMP build versions, and is also experimenting with using the CCP4i GUI to run CNS. If interested, leave him a message.

Troubleshooting

It was reported that due to an operating system bug in Mac OSX 10.5.x, the program may crash with

forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC        Routine            Line        Source             
cns_solve          003548DF  Unknown               Unknown  Unknown
cns_solve          00339FBB  Unknown               Unknown  Unknown
cns_solve          000F62EC  Unknown               Unknown  Unknown

Stack trace terminated abnormally.

This may occur if you are running the program with input redirection, but without output redirection, i.e.,

cns < test.inp

and the input file contains one ore more blank lines.

As a possible remedy, try:

cns < test.inp > test.out

Super-resolution and DEN

"Super-resolution" was defined in the DEN paper as achieving coordinate accuracy better than the resolution limit d_min of the diffraction data. This definition was proposed in analogy to its wide-spread use in optical microscopy: "super-resolution" methods such as STORM, PALM, and STED achieve accuracy of positions of fluorescent labels significantly better than the diffraction limit (in some cases, sub-nanometer accuracy - Pertsinidis, Zhang, Chu, Nature 466, 647-651, 2010).

DEN was found to be useful to move some atoms into correct positions in cases where electron density maps are difficult or impossible to interpret at low resolution. By default, DEN is active during the first torsion angle molecular dynamics stages, but then turned off during the last two stages. In addition, the DEN network is deformable. Thus, DEN is very different from "secondary structure" restraints or point restraints to reference models which are "on" all the time. Rather, DEN steers or guides the torsion angle conformational search process during refinement.

Selected references

• A.T. Brunger, P.D. Adams, G.M. Clore, P.Gros, R.W. Grosse-Kunstleve, J.-S. Jiang, J. Kuszewski, N. Nilges, N.S. Pannu, R.J. Read, L.M. Rice, T. Simonson, G.L. Warren,Crystallography & NMR System (CNS), A new software suite for macromolecular structure determination, Acta Cryst.D54, 905-921(1998).
• A.T. Brunger, Version 1.2 of the Crystallography and NMR System, Nature Protocols 2, 2728-2733 (2007).
• G.F. Schroeder, M. Levitt, and A.T. Brunger, Super-resolution biomolecular crystallography with low-resolution data, Nature 464, 1218-1222, 2010