[phenixbb] phenix and refmac5

anon phenix.ccp4 at googlemail.com
Tue Dec 15 03:02:48 PST 2009


recently i used phenix (AutoSol and AutoBuild) on a SAD dataset  
containing Iodine. I was wanting to do my refinement using Refmac  
instead of phenix.refine. I was wondering where would i be able to  
locate the correct .mtz file to input into Refmac5 for rounds of  
refinement? I was under the impression the .mtz file used for  
refinement was the one produced after scaling, but im not sure where  
phenix puts this.

Also I was wondering if anyone had any issues with phenix.xtriage  
carrying out its Matthews coefficient calculation? When using Phenix,  
it gave me a solution with 3 mols/AU, despite there being 4 mols/AU  
according to the Matthews coeffiecient calculation in CCP4. Looking  
back at the xtriage log in autosol it has n_residues= 200 (despite me  
not specifying anywhere the number of residues, my protein has 147  
residues). Realising this I re-ran Autosol, inputting my .mtz file  
along with my sequence this time, and specifying the number of NCS  
copies as 4. Looking at the phenix.xtriage log this time results in it  
recognising the correct number of residues, however the matthews  
coefficient calculation is still incorrect, claiming 1 mol/Au. Any  
ideas what may be the problem?

## Unit cell defined manually, will ignore
## specification in reflection file:
## From file :  None
## From input:  (140.124, 77.954, 54.519, 90, 98.549, 90)
## Space group defined manually, will ignore
## specification in reflection file:
## From file :  C 1 2 1
## From input:  C 1 2 1

Effective parameters:
#phil __ON__
scaling {
   input {
     asu_contents {
       n_residues = 588
       n_bases = None
       n_copies_per_asu = 4

Matthews coefficient and Solvent content statistics
| Copies | Solvent content | Matthews Coef. | P(solvent cont.) |
|      1 |      0.448      |      2.226     |       1.000      |
|              Best guess :    1  copies in the asu            |

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