Re: [PyMOL] rms commands

[Michael G. L. <ml...@um...>]

Hi,

I could be wrong about this, but there are a couple of very picky
alignment/fitting commands in PyMOL, and I think this is one of them.  If
it's one of the picky ones, it'll only work if everything about the two
selections looks the same.  In this case, your residue ids don't match up.
Can you try

alter object1, resi=3Dint(resi)+10
rms_cur (object1 and i. 30:39 and (name c,o,n,ca)), (object2 and i. 30:39 a=
nd (name c,o,n,ca))

to make sure that the residue ids match first?

-michael

--
This isn't a democracy;|                        _  |Michael Lerner
 it's a cheer-ocracy.  | ASCII ribbon campaign ( ) |   Michigan
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On Mon, 23 Aug 2004, Andreas [ISO-8859-1] F=F6rster wrote:

> Hey all,
>
> just the other day I discovered a nifty command in pymol.
>    rms_cur selection1, selection2
> determines the deviation between two (previously aligned) selections
> without doing a fit.  Here's what I do:
>    rms_cur (object1 and i. 20:29 and (name c,o,n,ca)), (object2 and i.
> 30:39 and (name c,o,n,ca))
>
> Hmmm, doesn't work.  Error:
>    ExecutiveRMS-Error: No atoms selected.
>
> OK, differnt try (debugging for beginners):
>    select selection1, (object1 and i. 20:29 and (name c,o,n,ca))
>
> So far so good.  Feedback:
>    Selector: selection "selection1" defined with 40 atoms.
>
> And again:
>    select selection2, (object2 and i. 30:39 and (name c,o,n,ca))
>
> Good again.  Feedback:
>    Selector: selection "selection1" defined with 40 atoms.
>
> Now I go for gold:
>    rms_cur selection1, selection2
>
> Arrgh, bummer:
>    ExecutiveRMS-Error: No atoms selected.
>
>
> What am I doing wrong??  I'm using pymol 0.95 under WinXPpro and pymol
> 0.95rh9 under linux/FC2.
>
>
> Andreas
>
>
> --
>                     Andreas F=F6rster
> Dept of Biochem, Univ of Utah, 20N 1900E, #2460 Eccles Bldg.
> Salt Lake City, UT 84132, phone: 001.801.585.3919
> home: 465 3rd Av, SLC, UT 84103, 001.801.364.0529
>         http://www.biochem.utah.edu/~andreas
>
>
>
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