Hi, We used to allow degenerate solutions (i.e. ones in which only the orientation is known but not the position, or in which the orientation and position within a plane perpendicular to a rotation axes are known), because these can be scored by the same likelihood target used for the rotation search. However, we never found these possibilities useful in practice compared to just doing a full translation search and they complicated the code tremendously, so these features were removed a couple of years ago. It seems we had missed a couple of places in the documentation of script files where they were still mentioned, but the documentation has just now been updated.
Best wishes, Randy Read On 9 Dec 2013, at 09:20, Rojan Shrestha <ro...@riken.jp> wrote: > Hello, > > Can somebody tell me how the Phaser degenerate function can be used with > MR_BTF? > > My script is as follows: > > #my_phaser_run.com > phaser << eof > TITLe BTF_RUN > MODE MR_BTF > HKLIn a.mtz > LABIn F=Fobs SIGF=Sigma > ENSEmble mol1 PDB a.pdb IDENtity 100 # this is model structure not solution > after MR > ENSEmble mol2 PDB b.pdb IDENtity 100 # this is model structure not solution > after MR > COMPosition PROTein SEQuence a.fasta NUM 1 > COMPosition PROTein SEQuence b.fasta NUM 1 > SOLUtion 6DIM ENSEmble mol1 EULEr 17 20 32 FRACtional 0.12 0.05 0.74 > SOLUtion TRIAl ENSEmble mol2 EULEr 22 25 40 DEGEnerate X FRACtional 0.05 > 0.74 > ROOT ab > eof > > … > > When I run this script, I got an error: > $TEXT:Script: $$ Baubles Markup $$ > TITLE GPCR_MR > JOBS 1 > ENSEmble mol1 PDB a.pdb IDENtity 100 # this is model structure not solution > after MR > ENSEmble mol2 PDB b.pdb IDENtity 100 # this is model structure not solution > after MR > COMPosition PROTein SEQuence a.fasta NUM 1 > COMPosition PROTein SEQuence b.fasta NUM 1 > SOLUtion 6DIM ENSEmble mol1 EULEr 17 20 32 FRACtional 0.12 0.05 0.74 > SOLUtion TRIAl ENSEmble mol2 EULEr 22 25 40 DEGEnerate > $$ > <B><FONT COLOR="#FF8800"> > $TEXT:Warning: $$ Baubles Markup $$ > ------------------------------------------------------------------------------------- > SYNTAX ERROR: Use (optionally) ZSCORE RFZ or PTNCS > ------------------------------------------------------------------------------------- > > Regards, > > > > Rojan > ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
