Re: [PyMOL] RMSD produced by align command

[Thomas E. <te...@mb...>]

Jason,

When I use optAlign I get the same value as with ProFit (4.615214 A.),  
that's why I suspected that 'align' omits some distant CA atoms when  
calculating the RMSD. In fact I just noticed that the last 2 residues  
are not assigned an asterisk or a dot in the alignment. So, when I  
exclude them from 'optAlign' I get 1.780601 A., the same value as with  
'align'.

Thomas


> Thomas,
>
> If PyMOL has paired two atoms for alignment, then they will be used in
> the calculation of the RMSD.
>
> Also, this sounds like you should be using 'fit' or 'optAlign' to be
> superposing the molecules.  (If you already know the atom pairings, no
> 'alignment' step is necessary.)
>
> Possibly helpful link:
> http://www.pymolwiki.org/index.php/Category:Structure_Alignment
>
> See: fit, optAlign, intra_fit_rms.
>
> Hope this helps,
>
> -- Jason
>
> --
> Jason Vertrees, PhD
>
> PyMOLWiki -- http://www.pymolwiki.org
>
>
>
> On Tue, Dec 29, 2009 at 1:27 PM, Thomas Evangelidis  
> <te...@mb...> wrote:
>> Dear pymol users,
>>
>> I'm trying to understand how align command measures the RMSD between 2
>> homologues and explain the discrepancy between that value and the one
>> obtained from ProFit. The sequence alignments produced by both
>> programs are continuous and match, but the RMS values are 1.781 and
>> 4.615 for Pymol and Profit respectively. The RMS corresponds to Ca
>> atoms only (pymol command line: "align 3G5U_A and name CA and chain A,
>> H_ABCB1_NBD1 and name CA, cycles=0, object=ao"). Does pymol consider
>> only Ca atoms that are closer than a default cutoff distance only
>> (e.g. 5 A) when calculating the RMSD?
>>
>>
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>


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