Revised May 6, 2004
CHIRality ANalysis for Oligonucleotides
Chirano checks that the stereochemistry of sugars corresponds to what is expected of beta-D-nucleosides or their 2'-deoxy derivatives, as defined by the IUPAC-IUB comission (1983 Eur.J.Biochem. 131:9-15), and it complains if it does not. Also, it checks the naming convention for the geminal protons; e.g., it will complain if H2' (pro-S) and H2" (pro-R) are switched in deoxyriboses. You may want to run this program for nucleic acids coming out of various simulation, refinement or modeling packages, to make sure that you simulated the molecule that you intended to. This program was written in 1993, when nothing of the sort was availbale to us. Now, there are other validation tools available, e.g., a validation web server at RCSB .
It must work with both RNA and DNA. You can download the executable from here for sgi, linux, or a somewhat old version for spark. For the James' group, the sgi version is in /optSGI/bin, the spark version is in /oldLOCAL/bin/nmr on picasso, and linux version is in /home/ulyanov/bin on warhol-nmr.
You type "chirano", and it will ask for the pdb file name, and then for the pdb format.
For DNA, there are 3 formats supported:
However, for RNA (or, for mixed DNA/RNA sequences), only Amber4.1 format is supported. In general, this option should be able to read most of pdb format variants (in the future, I will try to get rid of all options but this one). If nevertheless, there are some problems with atom names, try to run a csh script fixatoms on your pdb file. If this does not help, please send me the pdb file. Also, as this is a fortran program, it is presently compiled for a maximum of 300 residues. Hopefully, I will get rid of this limitation some time..
Program reports how many residues have been read from the pdb file, and it just exits if verything is OK. For example:
chirano
If there are problems, the program will report them: