Hi Patrick,
What other tool do you compare to and how large is the difference? There
are different ways to calculate the RMSD, and they may have some rounding
errors.
Cheers,
Tsjerk
On Fri, Oct 3, 2014 at 8:17 PM, PC <patrick.coss...@inbox.com> wrote:
> 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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--
Tsjerk A. Wassenaar, Ph.D.
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