Hi Sean,
Use 'fit' instead.
# get two sample proteins
fetch 1cll 1ggz, async=0
# show their object matrices
print cmd.get_object_matrix("1cll")
print cmd.get_object_matrix("1ggz")
# fit the first 26 AAs via alpha carbons
fit 1cll///4-29/CA, 1ggz///4-29/CA
# show the object matrices, again
print cmd.get_object_matrix("1cll")
print cmd.get_object_matrix("1ggz")
Let me know if this isn't what you need.
Cheers,
-- Jason
On Sun, Oct 10, 2010 at 1:32 AM, Sean Law <magic...@hotmail.com> wrote:
> Hi PyMOLers,
>
> I was wondering if this problem was exclusive for my case. I was using
> "pair_fit" (rather than super/align) to superimpose two conformations of the
> same structure and noticed two things:
>
> 1) After being superimposed, BOTH structures (source and target) end up
> moving rather than just one
>
> 2) The object matrix is not changed from identity for either source or
> target structures (even though both structures have moved)
>
> My question is whether there is a way to avoid having both structures move
> and only have the target move towards the source? If not, is there a way to
> ensure that the object matrix for both structures get updated after they are
> shifted?
>
> Thanks!
>
> Sean
>
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--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
------------------------------------------------------------------------------
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3.
Spend less time writing and rewriting code and more time creating great
experiences on the web. Be a part of the beta today.
http://p.sf.net/sfu/beautyoftheweb
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