Re: [ccp4bb]: Refine beginning in CNS followed by Refmac

[Joel Bard]

Hi Julia-   You might want to look into the phenix project:   http://www.phenix-online.org/   For one thing phenix.refine can do both simulated annealing and TLS and accepts a variety of reflection file formats (including .sca).  For another, if you want to go from hkl files to mtz files you can use iotbx.reflection_file_converter.  There's a whole GUI thing but it's probably easier to just use the command line tools available through the CCI Apps download.   Best,   Joel >>> "Julia Warren" <[EMAIL PROTECTED]> 10/10/2006 3:50:13 PM >>> Hi everyone, I am a relatively new user of Refmac and I have encountered a problem: I would like to begin my refinement with an annealing step in CNS, and then continue my refinement in Refmac because I would like to use TLS parameter.  My problem is that I would like to retain the RFree reflections designated at the beginning of my refinement and so cannot just begin in Refmac, which would automatically generate new RFree if I just started with my .sca file anew.  The CNS column labels when generating an .hkl file (and then a .cv file to create RFree tags) are INDEX (HKL), IOBS, SIGI, FOBS, SIGMA, and TEST.  I tried using the CCP4 program "F2mtz", with the option "Create full unique set of reflections and keep existing FreeR Data" so that I can retain the same set of reflections in my r-work vs. r-free, however I am afraid that I am running in to formatting errors (maybe?).  It seems that when I input data with the columns INDEX (HKL), IOBS, SIGI, and TEST (to be consistent with the default fortran formatting listed when "X-PLOR/CNS" is chosen as the import reflection file, just in case that was my problem), I receive the following error: Data line--- COMPLETE FREE= MtzParseLabin: run out of labels trying to match "FREE"  FREERFLAG:  Error in label assignments in LABIN The Fortran format listed for these six columns (H, K, L, IOBS, SIGI, TEST) is: '(6X,3F5.0,6X,F10.3,7X,F10.3,6X,F10.0)' I can see from the log file that the program has created the following column labels: H K L FUNI SIGFUNI IOBS SIGI TEST Is this a formatting problem?  If so, how can I get around this? Also, I tried running F2mtz but WITHOUT the option "Create full unique set of reflections" and although I receive no error, I notice that only these six columns are generated (HKL, IOBS, SIGI, and TEST) while mtz files created directly from the .sca file contain the following columns: (H K L FreeR_flag F SIGF DANO SIGDANO F(+) SIGF(+) F(-) SIGF(-) ISYM).  Is it a problem to use this mtz to continue my refinement in Refmac?  Will I run into problems if I try to export this mtz into a file that can be used say in Shelx? Is there any easier/better way to convert .hkl files with Rfree tags into mtz files that are acceptable to Refmac?  If I will use the program F2mtz, are there certain inputs to be especially careful about that it might be easy for a new-be to overlook?  I am using cns_solve_1.1 and Refmac5.0 Thanks for your help, Julia