[phenixbb] Whic mtz file to use and parameters for phenix.refine (GUI) to set?

Vellieux Frederic Frederic.Vellieux at ibs.fr
Mon Jul 19 05:13:03 PDT 2010

Hi Hermella,

The first thing (I think) you should do is to check your molecular 
replacement solution on the graphics station (use whichever software you 
feel most comfortable with): check the packing in particular, are there 
crystal-forming contacts that explain the crystal - if you have regions 
of void then it is likely that your solution is not a solution (you may 
have missing molecules for example). And you may also wish to model into 
the electron density coming out of Phaser (such as mutating residues, if 
the quality of the electron density map allows you to do that).

For this, you use the mtz file coming out of phaser, that contains the 
electron density map coefficients (SigmaA).

Also, if your search model is made up of several subunits, you will 
probably want to carry our rigid-body refinement (of the subunits 
independently) before carrying out any model building.

For refinement, I suggest that you use the initial mtz file (containing 
FP, SIGFP, FREERFLAG), unless you want to have (after X refinement 
rounds) a single mtz file that contains all the history of the structure 
determination work. But as long as the input mtz file (for refinement) 
contains the FP, SIGFP, FREERFLAG columns UNMODIFIED then it's a 
question of taste. I keep everything in separate directories myself, I'm 
used to that...


Hermella Woldemdihin wrote:
> Hi,
> I am new to phenix.refine. I'm using the graphical interface.
> I hav processed my dfiffraction data and used Phaser MR for molecular 
> replacement.
> And I goyt a result: a solution pdb file and the associated mtz file.
> 1. So I use the mtz file from this Phaser MR solution or the original 
> file from my data
> processing in phenix.refine?
> 2. I have set parameters for phenix.refine like this:
> Is there other settings for the parameter which I should do for a 
> better result?
> PDB data: my solution from Phaser MR
> XRAY DATA= ????
> Simulated Annealing=1000
> Update waters
> Refine Target weights: Wxc=0.8 Wxu=1.6
> Cycles=5
> Fix rotamers
> Fix bad side chains
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