strange MR problem

From: intekhab alam
Date: 13 December 2011 04:26

Hi All

 

I have a 3.0A dataset of a protein-protein complex. I used one of the protein structure solved previously as a template and used phaser in CCP4 as well as in phenix. I used the sca file in phenix which gave a solution with 6 monomers in ASU which are packed as a hexamer. In ccp4 phaser i used the converted .mtz file which gave 6 molecules in ASU but with a different packing. In both the cases map fits well in the model and there is some extra density that may correspond to second protein partner of the complex molecule. when i tried to use the MR solution generated in phenix with the mtz file from ccp4 the model shows a lot of clashes.

 

what kind of approach should i take so as to resolve this ambiguity.

 

Regards

--
INTEKHAB ALAM
LABORATORY OF STRUCTURAL BIOINFORMATICS
KOREA UNIVERSITY, SEOUL

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From: Tim Gruene

Dear   ,

Can you clearify what you mean by the sentence
file from ccp4 the model shows a lot of clashes"?

I do not understand what you need the mtz file for in order the check
for clashes.

At 3A you may have serious model bias and one or both of the solutions
may not be correct.
The best would be to try and fit the second protein (by MR, or if only
the sequence is known, try e.g. buccaneer). If your R/Rfree eventually
drop below, say, 40%, you are probably on the right track.

Tim

- --
- --
Dr Tim Gruene

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From: Eleanor Dodson


csymmatch pdbin-ref my_favorite.pdb pdbin the-other.pdb -origin-hand

This should move the-other.pdb to overlay my-favorite.pdb

It WONT relabel the Chain IDs though..

Eleanor