One should emphasize that this alignment is a *sequence* alignment in
case of the "align" command.
Cheers,
Thomas
On 11/30/2011 11:19 AM, Tsjerk Wassenaar wrote:
> Hi Martin,
>
> It does an alignment, finding matching pairs of atoms, removing
> outliers and calculating the RMSD over the remai
Hi Martin,
It does an alignment, finding matching pairs of atoms, removing
outliers and calculating the RMSD over the remaining matches.
Cheers,
Tsjerk
On Wed, Nov 30, 2011 at 11:05 AM, Martin Hediger wrote:
> How does PyMOL calculate the RMSD between two structures where the
> number of atoms
How does PyMOL calculate the RMSD between two structures where the
number of atoms is different?
Martin
Am 11.11.11 14:59, schrieb Thomas Holder:
> Hi Martin,
>
> is it the transform=0 argument what you are looking for?
>
> http://pymolwiki.org/index.php/Align#PYMOL_API
>
> x = cmd.align('fo
Hi Martin,
It should be RMSD indeed. Mind that the final RMSD from align is obtained
after optimizing the fit by leaving out outliers.
Cheers,
Tsjerk
On Nov 29, 2011 10:07 AM, "Martin Hediger" wrote:
Is the RMS the same as RMSD? PyMOL writes "RMS" when using align.
Martin
Am 11.11.11 14:
Is the RMS the same as RMSD? PyMOL writes "RMS" when using align.
Martin
Am 11.11.11 14:59, schrieb Thomas Holder:
> Hi Martin,
>
> is it the transform=0 argument what you are looking for?
>
> http://pymolwiki.org/index.php/Align#PYMOL_API
>
> x = cmd.align('foo', 'bar', transform=0)
> print '
Hi Martin,
is it the transform=0 argument what you are looking for?
http://pymolwiki.org/index.php/Align#PYMOL_API
x = cmd.align('foo', 'bar', transform=0)
print 'RMSD:', x[0]
About the "some kind of refinement": There are arguments "cutoff" and
"cycles" that control this behaviour.
Cheers,
Dear List.
When aligning two structures using the PyMOL align command, one gets a
final RMS value indicating some kind of "convergence" i would say. Can I
somehow access the function for calculating this value directly from the
pymol prompt without aligning?
Thanks for hints
Martin
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