[phenixbb] table 1 no CC values, selenomethionine occupancy refinement

Georg Mlynek georg.mlynek at univie.ac.at
Thu Apr 4 11:22:06 PDT 2013

Dear All, I have 3 minor questions/problem and would be grateful for 
some help.

1a. Providing the XDS_ASCII.HKL to phenix tableI works perfect, however 
there are no values written for CC1/2. The same file in 
phenix.merging_statistics I get the CC1/2. Am I missing something?

1b. The only value phenix tablel one takes from INTEGRATE.LP (i guess  
CORRECT.LP will work too) is the wavelength - true?

2. I see some negative density around the seleniums in my 
selenomethionine labeled protein. I guess this is due to radiation 
damage. Is the accepted standard to do occupancy refinement for just the 
sidechain, or just parts of the sidechain, the whole residue  or just 
leave it like it is.

For the side chain

refinement.refine.occupancies {
   constrained_group {
     selection = resname MSE ( name CB or name  CG or name SE or name CE 
or name HB2 or name HB3 or name HG2 or name HG3 or name HE1 or name HE2 
or name HE3

should work or?

I am using version dev-1334 on ubuntu.

Best regards Georg.

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