Re: [ccp4bb]: Morphing with LSQMAN

[Nat <nathaniel.echols@yale.edu>]

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> Thanks for the messages; however, I might not have explained myself
> properly. Basically I have a 2 domain protein. I want to keep one domain
> fixed in space, but the other domain to move. Within the fixed domain, a
> cofactor undergoes torsion (with part of it fixed in space). The PDB files
> made by LSQMAN (from INTERNAL morphing) are pre-superimposed (I think). I'd
> like to avoid any superimposition, and have the same results as CARTESIAN
> morphing gives (this works perfectly for the protein, but not for the
> cofactor).

Have you tried using X-PLOR or CNS to perform adiabatic mapping instead?
It will certainly take much longer than LSQMAN, but this will allow you to
keep the original coordinate sets.  I have a CNS script that will do this;
email me if you're interested (the important part is less than ten lines).
I've been meaning to eventually write a tutorial akin to what Gerard has
on his page.

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Nathaniel Echols                                                  Programmer
nat@bioinfo.mbb.yale.edu                                        Gerstein Lab
203-589-6765                                                 Yale University
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