Compared to searching against the entire PDB, which entails the same problems specified below,
finding a high propensity contaminant in a targeted search would be faster in any case. A coarse classification by
expression host (coli, sf, etc) might further accelerate the search.
The strategy is the same as in crystallization: minimize the experiments likely to fail (pretty sure
the T-cell receptor is not an e coli contaminant) but screen the rest comprehensively.
That is a simple way to beat the odds. I am sure there are many, more thought-through,
ways to achieve this, but the concept holds.
Cheers, BR
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Huw Jenkins
Sent: Friday, September 02, 2016 2:02 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] Another pifall of MR
On 2 Sep 2016, at 20:56, Bernhard Rupp (Hofkristallrat a.D.) <[log in to unmask]> wrote:
>> Or are you saying you’d like something like this put into the standard pipelines?
>
> Exactly - something like this would be a useful (default) option in the MR packages.
The issue with this as a default is devising a reliable way to identify and stop (what would become) long running searches for multiple copies of the wrong contaminant in a large asymmetric unit without missing novel crystal forms of a known contaminant.
Huw =
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