[phenixbb] automr with muti components (NMR models)

[Partha Chakrabarti]

Hi Ming,

Just to share an experience:

I did a MR with NMR model using Phaser (which is I guess the backbone in
phenix autoMR) where the identity was close to 100 % and had a similar
situation. The Z score was about 4 and it did not look like fitting to the
density. The only positive thing was that the cell dimensions and symmetry
looked right. That might be the first thing to check.

Then displayed the whole molecule in coot and did a real space fitting. That
made one hell of a change. The trick is, if you do the real space fitting on
a small area, you see what is the script that is running, copy that and run
the script changing the amino acid numbers (i.e, taking the whole thing,
1-n).

For the multidomain case, are you sure that there is no funny clash? The
solution might look much worse in that case. It just might be worth to try
combinations of two domanins, not three, for example, domain A and C.

Best, Partha



On Dec 3, 2007 6:47 AM, ming lu <ming2000cn at gmail.com> wrote:

> Hi everyones
>
> I am trying automr to solve the structure of my protein. It has three
> domains, each domain has NMR structure available. So the sequence identity
> of my search model is 100%. I tried use mutiple components as search models,
> but I had a hard time to obtain a interpretable solution. Any suggestions on
> the use of mutiple components as search models? or suggestions on how to use
> NMR structure as search models? Thanks for your help.
>
> Ming
>
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> phenixbb at phenix-online.org
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>
>


-- 
MRC National Institute for Medical Research
Division of Molecular Structure
The Ridgeway, NW7 1AA, UK
Email: pchakra at nimr.mrc.ac.uk
Phone: + 44 208 816 2515
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