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[ccp4bb]: Re: your mail



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On Wed, 1 Nov 2000, Palmira daSilva wrote:

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> 
> Hi dear all:
> 
> I have three complexes of a 45 KD Fab ( two domains with a flexible hinge 
> region). Two of them are solved, the third has been a headache for some 
> time now.

> 1) How do I perform a search for my 4 molecules allowing for flexibility in 
> the hinge region?

In the Classical Fab molecular replacement mode, one would search with
just the Fv and Constant (Cl+Ch1) domains separately.   This neatly
resolves the problem if the smaller models can be pulled out of the
rotation and translation function lists.  Quite a few Fab structures have
been solved by this method.  If you have a 100% sequence-identical model
you could do quite well by this method.

An alternative is to take all existing Fab structures (back when I was
doing them there were fewer), superimpose them on a common Fv framework,
substitute your Fv for their Fvs, then substitute your Const regions for
their constant regions.  Et viola !  You get automatically generated
models of different Fabs with different elbow domains.  You can
then use these as search models, or if you already have Fv domain
solutions you can use each of them as starting points for rigid body
refinements.  Something close to this technique pulled out the constant
regions for BR96 back when I tried it, even though the constant regions
were somewhat disordered.  It does involve a certain amount of renumbering
or automatic alignment methods, but it all depends how desperate you get.

If all else fails, invoke the curse of the 26-10 Fab (a P21 xtal form
twinned such that it superficially appeared to be C2221) and crush the
xtals underfoot.

Good luck,
Phil
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| Phil Jeffrey                                  |                             |
| Crystallography Facility Manager              | If you lie to the compiler, |
| Memorial Sloan-Kettering Cancer Center, NYC   | it will get its revenge     |
| phil@xray2.mskcc.org                          |     - Henry Spencer         |
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