Thanks for the many emails I have received. Particularly to Ed who wrote and posted a script to the board and other
people who offered to do it over the weekend.
I have achieved what I want with the unsupported ccp4 program compar (Plea to CCP4 support- increase the array sizes by
an order of magnitude or two in the distributed binaries- modern machines will be fine with this). If you turn on
monitoring of bad fits with a cut of 0.001 Angstrom then you get distance with every pair of atoms with the same name
in the log file. This can be extracted and imported into excel for ordering by size.
Most comparison programmes assume you want to move the structures to give the best fit before calculating the stats
whereas I wanted not to move them to see the effect of the molecular replacement. I also wanted the individual atom
pairs not the average by residue etc.
The other responses are summarised below but I have not tested them.
Ed has posted his script to the board.
Other suggestions- I have not tested these
-----------------
you could you the distance matrix to compare two stricture.
In R there is a package bio3d that read the pdb's file and calculate the matrix.
http://www.r-project.org/
http://mccammon.ucsd.edu/~bgrant/bio3d/
---------------------------------
Maybe Profit (http://www.bioinf.org.uk/software/) could be your friend ?
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Looks like SSM should do that, just google on SSM
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LSQMAN has a bunch of analysis and plot options. It always applies the current LSQ operator on one of the molecules, but
as long as you don't do any superposition, that will be the identity operator.
http://xray.bmc.uu.se/usf/lsqman_man.html
-----------------------------------------------------
--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck, University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX
email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852 (Room G57 Office)
020-7631-6800 (Department Office)
Fax 020-7631-6803
If you want to access me in person you have to come to the crystallography
entrance
and ring me or the department office from the internal phone by the door
