RE: [PyMOL] align output

Andreas

>  ExecutiveAlign: 2889 atoms aligned.
>  ExecutiveRMS: 95 atoms rejected during cycle 1 (RMS=3D6.10).
>  ExecutiveRMS: 152 atoms rejected during cycle 2 (RMS=3D2.98).

means:

2889 atoms were aligned intially, then after looking at the quality of =
the
alignment, 95 atoms were rejected as outliers and the alignment was run
again with 2794 atoms.  On cycle two, 152 more atoms were rejected and =
the
fit was performed with the remaining 2642 atoms with a final RMS of =
2.98.

align (protein1 and name ca), (protein2 and name ca), object=3Dalignment

will show you visually the atoms used in the final fit.

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
400 Oyster Pt. Blvd., Ste 213
South San Francisco, CA 94080
(650)-346-1154  Fax:(650)-593-4020
 =20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Andreas F=F6rster
> Sent: Wednesday, September 29, 2004 8:23 AM
> To: pymol
> Subject: [PyMOL] align output
>=20
> Hey Warren, world,
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> I want to make sure that I understand the output from the=20
> align command correctly.  Here is an example:
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> align (protein1 and name ca), (protein2 and name ca)
>  Match: read scoring matrix.
>  Match: assigning 3194 x 3010 pairwise scores.
>  MatchAlign: aligning residues (3194 vs 3010)...
>  ExecutiveAlign: 2889 atoms aligned.
>  ExecutiveRMS: 95 atoms rejected during cycle 1 (RMS=3D6.10).
>  ExecutiveRMS: 152 atoms rejected during cycle 2 (RMS=3D2.98).
>=20
>=20
> Does this mean that in the end, 2642 atoms (2889 - 95 - 152)=20
> are aligned?  Or are 2889 atoms aligned?
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> Thanks
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> Andreas
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> --=20
>                     Andreas F=F6rster
> Dept of Biochem, Univ of Utah, 20N 1900E, #2460 Eccles Bldg.
> Salt Lake City, UT 84132, phone: 001.801.585.3919
> home: 465 3rd Av, SLC, UT 84103, 001.801.364.0529
>         http://www.biochem.utah.edu/~andreas
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