Hi Aaron, Since distortion from standard DNA conformation is measured by rigorously calculating a number of different parameters at numerous levels (base pair level, dinucleotide level, overall helical form, etc.), I believe your best bet would be to run your structure through 3-DNA (which also includes results from 7 different DNA structure analysis programs) to identify what features of your distorted structure that you most want to emphasize and then use a standard graphics program (3-DNA will also do this, Ribbons and others) to highlight/color those distorted areas that you want to focus on. http://rutchem.rutgers.edu/~xiangjun/3DNA/
Although a standard reference frame is used to calculate all these parameters, there is no numerical figure applied to the overall DNA structure to represent its departure from standard conformation so I don't think there is any program that can make a color-coded picture automatically. Regards, Debanu. -- Debanu Das, Scientist, JCSG, Stanford Synchrotron Radiation Lab, California. -----Original Message----- From: CCP4 bulletin board on behalf of Aaron Oakley Sent: Wed 6/13/2007 10:02 PM To: [email protected] Subject: [ccp4bb] Program for colouring DNA Colleagues, I am interested in making a figure of a recently solved protein-DNA complex, such that the DNA is colour-coded according to its degree of distortion away from classic B-DNA. Is anyone aware of a program that can do this? With thanks, Aaron Oakley
