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
>
> show sticks, loop*
>
> print cmd.pair_fit("loopACA", "loopBCA")
>
> Cheers,
> Warren
>
> -----Original Message-
> From: Thomas Evangelidis [mailto:te8...@mbg.duth.gr]
> Sent: Wed 10/28/2009 8:09 PM
> To: pymol-users@lists.sour
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
en
-Original Message-
From: Thomas Evangelidis [mailto:te8...@mbg.duth.gr]
Sent: Wed 10/28/2009 8:09 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] how to get RMSD from align command
Simple question, it must have been answered before but couldn't find
it so far:
how can
Simple question, it must have been answered before but couldn't find
it so far:
how can I get the RMSD value from the align command in a python
script? cmd.align() returnes a tuple of 8 numbers and none of them is
the actual RMSD value I get when I align these 2 structures manually.
thanks,
