Hi Robert,

This is pretty easy to do in Chimera using the "Values at Atom Positions" and "Render by Attribute" dialogs. Here's a video showing how.

http://www.cgl.ucsf.edu/chimera/videodoc/MapValues/index.html

This and more videos are on the Chimera video tutorial web page

http://www.cgl.ucsf.edu/chimera/videodoc/videodoc.html

Tom

I was wondering if there was a script available that would get the map density values of amino aid residues in a model fitted to an EM or X-ray density map and then write the data to a text file?

Essentially what I need is something that does something like this (but not laboriously by hand)

e.g. in command line mode

select #1:1.B

then I use Tools>Volume Data>Fit in Map and click 'Update' to get the average map density value for the atoms in amino acid residue number 1 in chain B of model 1.

Many thanks for your help

Bob Ford, Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, 131 Princess St., The University of Manchester Manchester M1 7DN, UK.

Tel: +44(0)161 2004187 Fax: +44 (0)161 3068918 bob.ford@manchester.ac.uk www.ls.manchester.ac.uk

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