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... Fred. 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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