the job.
Cheers,
Warren
> -Original Message-
> From: Thomas Evangelidis [mailto:te8...@mbg.duth.gr]
> Sent: Thursday, October 29, 2009 4:56 PM
> To: Warren DeLano
> Cc: Thomas Evangelidis; pymol-users@lists.sourceforge.net
> Subject: RE: [PyMOL] how to get RMSD from ali
nt: Thu 10/29/2009 5:24 AM
> To: Warren DeLano
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] how to get RMSD from align command
>
> Hi Warren,
>
> Now I am more confused. I used align command to measure the overall
> RMSD between homologous structures. Apparently ali
/29/2009 5:24 AM
To: Warren DeLano
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] how to get RMSD from align command
Hi Warren,
Now I am more confused. I used align command to measure the overall
RMSD between homologous structures. Apparently align is not
appropriate if not
Hi Warren,
Now I am more confused. I used align command to measure the overall
RMSD between homologous structures. Apparently align is not
appropriate if not sufficient sequence similarity is present. I later
came across CEalign plugin, which does structure-based
superimposition. This comm
Hey Thomas,
if you want to use align anyway, make sure to use the quite=0 option.
The "quiet" option (if present) is set to zero by default for parsed
PyMOL commands, but is not set for Python API calls.
align
is nearly equal to
cmd.align(quiet=0)
Thus, if you want to get rmsd output, include qu
Tom,
The complication with cmd.align() is that it is doing a whole lot more than a
simple alignment. The first number is in fact the RMS, but it covers only the
subset of the input atoms remaining after refinement is completed. The count of
aligned atoms is the second field.
If you're looking
