Re: [PyMOL] Align in PyMOL via Python script

[Irwin S. <irw...@po...>]

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 <bio...@gm...>
Sent: Thursday, March 2, 2023 8:24 AM
To: pym...@li... <pym...@li...>
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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