Hi,<br><br>I&#39;m a new Phenix user, so please forgive me if I ask an obvious question...<br><br>I have pretty good SIRAS phases from one derivative, and calculating difference maps for 2 other derivatives show decent peaks above 5 sigma in both these maps. I&#39;ve tried to follow the MIR example, but no sites are found in the two other derivatives (I thought Phenix calculates difference Fouriers for other derivatives as soon as it finds sites in one of the datasets - but it doesn&#39;t appear to in my case). Anyway, the following is my effeort at trying to use the SIRAS phases of the good derivative and the 5sigma peaks in the 2 other derivatives to phase a better map. Please could someone advise me if this script won&#39;t do what I&#39;d like it to (i.e., calulate difference Fouriers for derviatives 2 and 3, refine the HA sites that I&#39;ve included, and calculate phases):<br>

<br>cell 100.000 100.000 100.000 90.000 90.000 90.000 # cell params<br>resolution 5.5&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #&nbsp; Resolution<br>solvent_fraction 0.47<br>input_seq_file seq.dat<br>##### READ IN DERIV 1 SIRAS PHASES ######<br>

input_phase_file solve_4.mtz<br>input_phase_labels FP SIGFP PHIB FOM HLA HLB HLC HLD<br>############### DERIV 2 #################<br>input_file_list nat.sca hg.sca&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #&nbsp; Native&nbsp; and deriv 2<br>nat_der_list&nbsp;&nbsp;&nbsp; Native&nbsp; Hg&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # identify files by ha type<br>

inano_list&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; noinano&nbsp;&nbsp; inano&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # say if ano diffs to be used<br>f_prime&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -2.1<br>f_double_prime&nbsp; 9.5<br>n_ha_list&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp; 6&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # number of heavy-atoms<br>sites_file&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; hg-sites.xyz<br>

run_list&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; start&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # read in datafiles for dataset<br>run_list&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; read_another_dataset&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # about to start a new dataset here<br>############### DERIV 3 #################<br>input_file_list nat.sca xe.sca&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #&nbsp; Native&nbsp; and deriv 3<br>

nat_der_list&nbsp;&nbsp;&nbsp; Native&nbsp; Xe&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # identify files by ha type<br>inano_list&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; noinano&nbsp;&nbsp; inano&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # say if ano diffs to be used<br>f_prime&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -0.1<br>f_double_prime&nbsp; 3.5<br>n_ha_list&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp; 11&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # number of heavy-atoms<br>

sites_file&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; xe-sites.xyz<br>##########################################<br>
<br>Many thanks!<br>