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Re: [ccp4bb]: Morphing with LSQMAN
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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).
I hope that explains my situation better.
Thanks again
>> Does anyone know if it is possible to switch off the superimposition
>> routine in the "INTERNAL" morph option in LSQMAN? Otherwise, is there
>> an easy way to rotate the intermediate PDB files produced by LSQMAN to
>> compenase. "CARTESIAN" morphing distorts the bound ligand, so I can't
>> follow that option.
>
> do you mean in the lsqman macro that the morph command generates ? you
> could just ignore it and not execute it. but with internal
> coords, the position and orientation of your intermediate models
> is not well-defined - that's why the superpositioning is done
> (well, recommended) in the first place
>
> --dvd
>
> ******************************************************************
> Gerard J. Kleywegt
> [Research Fellow of the Royal Swedish Academy of Sciences]
> Dept. of Cell & Molecular Biology University of Uppsala
> Biomedical Centre Box 596
> SE-751 24 Uppsala SWEDEN
>
> http://xray.bmc.uu.se/gerard/ mailto:gerard@xray.bmc.uu.se
> ******************************************************************
> The opinions in this message are fictional. Any similarity
> to actual opinions, living or dead, is purely coincidental.
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