Superimposing crystal structures?

Victor Jongeneel vjongene at isrec-sun1.unil.ch
Thu Sep 8 08:55:47 EST 1994


In article <34ian9INNu6t at sat.ipp-garching.mpg.de> krasel at alf.biochem.mpg.de (Cornelius Krasel) writes:
>From: krasel at alf.biochem.mpg.de (Cornelius Krasel)
>Subject: Superimposing crystal structures?
>Date: 6 Sep 1994 18:00:09 GMT


>Hello netters,

>I would like to superimpose different crystal structures in PDB format.
>I know that there are programs who can do that, but I would like to do
>it on a Linux box (e.g. to view the superimposed structures later
>in Rasmol). I understand that I have to minimize the RMS between different
>points (e.g. Calpha) but I am not sure _how_ to do this. I am especially
>unsure if commonly used algorithms can account for the relative
>orientation of a three-dimensional structure to another. (As you might
>see, my mathematical background is virtually nonexistant :-)

>Can anybody give me some hint (or even better, lead me to some piece of
>C source code)?

Manuel Peitsch at Glaxo Geneva (mcp13936 at ggr.co.uk) has written a 
homology-based protein modelling package called ProMod which contains a module 
that does just this.  As far as I know, the source code is in Fortran 77, so 
should be compilable on a Linux box.  I have done quite a few structure 
superimpositions with ProMod, and it is "totally automagic".

You may want to ask Manuel if he will make the code available to you.  He 
certainly does for the executables (anon FTP to expasy.hcuge.ch, SGI 
executables).

Good luck!

Victor J.





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