Re: [modeller_usage] Good Quality Score

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 7/26/11 8:33 PM, Brian Tsui wrote:
> In the Madhusudhan paper, the cutoff was at least 70% for a SO of 3.5 A.

Do you mean the SO was 70% for a cutoff of 3.5A?

> What number does that correspond to in the salign output?

The percentage of equivalent (i.e. within the cutoff) positions is the 
qscorepct member of the SalignData object returned by salign(). Set the 
cutoff with the rms_cutoff argument. And make sure you have QUALITY in 
the output argument.

> For the quality score, is there an objective number that I can use for
> every alignment to see whether it is good or not?

As I said, only for structure alignments.

> Lastly, for "iterative salign," is it recommended to run the regular
> version first or just jump straight to using the iterative salign? The
> Madhusudhan paper seems to forgo the use of iterative salign if the
> alignment is 70% at a SO of 3.5

I'm assuming you're looking at fig 1 in the paper here. There are three 
iterative procedures within that flowchart; one of them is skipped if 
the first procedure (simpler alignment using a subset of features) found 
a reasonable starting guess for the last procedure (structural 
alignment). The second procedure is simply an attempt to improve this 
guess if the first failed.

	Ben Webb, Modeller Caretaker
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