Re: [ccp4bb] Program for colouring DNA

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Program for colouring DNA
From: Aaron Oakley oakley {- at -} RSC {- dot -} ANU {- dot -} EDU {- dot -} AU
Date: 2007-06-14

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Subject: Re: ISSUE RESOLVED - REFMAC converts alpha-L-fucose into beta-L-fucose]
From: Kim Henrick henrick {- at -} EBI {- dot -} AC {- dot -} UK
Date: 2007-06-14

Subject: Re: Program for colouring DNA
From: "Das, Debanu" debanu {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2007-06-14

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: CCP4BB@JISCMAIL.AC.UK
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

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Program for colouring DNA
From: Aaron Oakley oakley {- at -} RSC {- dot -} ANU {- dot -} EDU {- dot -} AU
Date: 2007-06-14

Next message:
Subject: Re: ISSUE RESOLVED - REFMAC converts alpha-L-fucose into beta-L-fucose]
From: Kim Henrick henrick {- at -} EBI {- dot -} AC {- dot -} UK
Date: 2007-06-14