[o-info] Applying transformation in lsqman

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achandlr@uci.edu

Aaron Chandler wrote:

> Dear O users,
>
> I have a question regarding lsqman.  I am doing a least squares fit of
> one nucleic acid onto another.  For one, I have each atom of each base,
> and for the other, I have only the phosphorous atoms.  Even after
> defining that I want to use only these P atoms in an "explicit" with a
> "ATom_types PHosphorous" command, the program still complains "ERROR ---
> Different nr of zones ".   How can I get around this?
>
> Sincerely,
> Aaron Chandler
>
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It's me again (the original author of the letter attached).  Question #2 -
I got the "explicit" to work the way I described, but how do I actually
apply it in order to generate a pdb file for the transformed molecule?  It
should be something like the lsq_obj or lsq_mol commands from O, but I
haven't found anything in this vein.  I've saved the transformation as an O
datablock file, but what can I now do with it since lsqman doesn't even
prompt me for either it or the transformation file name itself when I use
the "apply" command?

Thanks,
Aaron

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