Maybe this is related to
http://www.biopython.org/pipermail/biopython-dev/2010-October/008361.html
Cheers,
Tsjerk
On Fri, Oct 3, 2014 at 8:37 PM, PC <patrick.coss...@inbox.com> wrote:
> Hi Tsjerk and others,
>
> Thank you, I did use PYMOL with cycles=0
>
> Online tools I used were:
> 1) Superpose
> 2) RMSDCalc from http://www.igs.cnrs-mrs.fr
> (not working now due to maintenance)
>
> I also used biopython. PYMOL def differs from biopython value.
>
> Thank you,
>
>
> -----Original Message-----
> *From:* tsje...@gmail.com
> *Sent:* Fri, 3 Oct 2014 20:23:59 +0200
> *To:* patrick.coss...@inbox.com
> *Subject:* Re: [PyMOL] align and RMSD calculation
>
> 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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