Hi,
Thanks, that's sorted it.
A follow up question is that when printing the results of the align command,
I've noticed that the number of cycles seems to max out at 1 regardless of what
I set it to - is that because it's reaching convergence after the first cycle?
All the best,
Irwin
From: Tamas Hegedus
Sent: Thursday, March 2, 2023 8:24 AM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Align in PyMOL via Python script
Hi,
You probably use the script version. In this case you have to use "print"
cmd: align x, y
output: ... Executive: RMSD =4.030 (10847 to 10847 atoms)
cmd: print(cmd.align("x", "y"))
output: (4.0296430587768555, 10847, 5, 24.87837028503418, 13476, 1234.0, 1192)
Bests, Tamas
On 2023. 03. 02. 8:54, Irwin Selvam wrote:
Hi,
I would like to run the Align Python script found on the Align page of the
PyMOLwiki (https://pymolwiki.org/index.php/Align). I've tweaked it slightly for
my uses and it seems to run fine on PyMOL 2.5.0 but according to the wiki it
should output a list of results (RMSD etc) in the internal feedback (or command
prompt?), but it doesn't in my case. Does anyone know why? It does seem like
there some missing lines to the script in order to achieve this. Apologies for
the basic question!
All the best,
Irwin
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