Re: [PyMOL] align and RMSD calculation

[PC]

Hi,

Sorry its me again. Can someone tell me where I can find the code for the align command?

It seems the RMSD differs from other online tools I found.

Thank you 

-----Original Message-----
From: patrick.coss...@inbox.com
Sent: Fri, 3 Oct 2014 09:15:17 -0800
To: patrick.coss...@inbox.com, pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] align and RMSD calculation

Ignore this question, I found the answer it setting cycles=0.

Thank you 

-----Original Message-----
From: patrick.coss...@inbox.com
Sent: Fri, 3 Oct 2014 07:55:31 -0800
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] align and RMSD calculation

Hi everyone,

I was using align in PYMOL and wanted to calculate RMSD.

But, PYMOL gave the following result:

MatchAlign: aligning residues (696 vs 696)...

 ExecutiveAlign: 2177 atoms aligned.

 ExecutiveRMS: 73 atoms rejected during cycle 1 (RMS=0.38).

 ExecutiveRMS: 103 atoms rejected during cycle 2 (RMS=0.13).

 ExecutiveRMS: 105 atoms rejected during cycle 3 (RMS=0.08).

 ExecutiveRMS: 66 atoms rejected during cycle 4 (RMS=0.07).

 ExecutiveRMS: 32 atoms rejected during cycle 5 (RMS=0.07).

 Executive: RMS =    0.063 (1798 to 1798 atoms)

How can I calculate the RMS WITHOUT PYMOL throwing atoms away in attempt to improve the RMS?

I want the raw number.

Thank you

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