refine rigid body to coordinates example, please

matsmcfly

Hi,

I have managed today, with the help of a colleague, to stumble our way though to complete a rigid body refinement. However, the main problem we had was in the initial refinement against the input structure (cif coordinates).

We were trying to use the following example (http://topas.dur.ac.uk/topaswiki/doku.php?id=matching_a_rigid_body_to_a_known_fragment), but were unclear on what exactly we needed to add to the example shown for our needs. Does anyone happen to have a real and complete example of the use of this for the start of a Rietveld rigid body refinement and would be willing to share?

I can share the basis of our input file if this would be useful.

Thanks,
Martin

johnsoevans

There's a little bit more on this in Chapter 6.3.8 of the Topas book Robert, Andreas and I put together (http://topas.dur.ac.uk/topaswiki/doku.php?id=book).

I don't have an example to hand, but the idea is Alan describes in the wiki post you cited.

Essentially you have some initial guess of the sites (he called these wC1, wC2). You can put these at 0 occupancy so they don't later influence the fit tot the data.

You then have the "real" sites that are described by the rigid body (C1, C2).

You write a set of distance restraints so that C1 is close to wC1, C2 is close to wC2 etc.

You then use only_penalties to minimise the differences.

You then have your starting positions and angles for the rigid body.

matsmcfly

Hi John,

Thank you for your reply, as chance would have it I ordered the book this morning after having looked at it for a while now.

If I recall correctly, we set up the rigid body and use these positions as the 'real' sites (C1, C2 etc). We then used the coordinates from a known structure (cif file) as a guess at the positions.

As I said, we did get it working, but this more through luck than judgement (I suspect) as we didnt know what was expected example i.e. in the gaps left '...'

When the book comes through I will take a look at the example your suggest (Ch 6.3.8), this might shine more light on things and then hopefully I will understand a bit better.

matsmcfly

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