You can View input command file, when working from the GUI. Could you cut and paste this into your message - obviously some inmportant parameter is not set, but I cant tell which without seeing that file.
Eleanor On 20 June 2012 05:25, Appu kumar <[email protected]> wrote: > Thank you for your reply, > I am running Malphare through CCP4 GUI interface. I am giving mtz file > and Se.pdb file as input and running it. I do not know running Malphare > through script. Please help me with heavy atom refinement in Malphare. > > On 20 June 2012 03:49, Pete Meyer <[email protected]> wrote: > >> It's not clear without looking at your input script, but it appears that >> you've got a problem with either your LABIN, ATREF or ATOM lines. It might >> be helpful to check out some of the example scripts distributed with ccp4. >> >> Pete >> >> >> Appu kumar wrote: >> >>> Dear CCP4 user, >>> I am facing problem in running Mlphare >>> for HEAVY ATOM REFINEMENT and PHASE CALCULATO. It is running successfully >>> but in output log file i am not getting any FOM for acentric. Log file >>> output of one of the cycle is >>> >>> *** Finished refinement cycle 3 >>> 0 reflections were rejected for refinement >>> >>> Figures of merit as functions of resolution shell >>> ------------------------------**------------------- >>> Resolution of each shell in angstroms: >>> 19.88 11.81 8.40 6.52 5.33 4.50 3.90 3.44 >>> >>> Number of Measurements phased -ACENTRIC >>> TOTAL >>> 20 107 280 498 721 1092 1383 1342 >>> 5443 >>> Mean Figure of Merit >>> 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 >>> 0.0000 >>> >>> Number of Measurements phased -CENTRIC >>> TOTAL >>> 29 62 98 120 139 161 158 145 >>> 912 >>> Mean Figure of Merit >>> 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 >>> 0.0000 >>> >>> Number of Measurements phased -ALL >>> TOTAL >>> 49 169 378 618 860 1253 1541 1487 >>> 6355 >>> Mean Figure of Merit >>> 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 >>> 0.0000 >>> >>> >>> Compound 1 "Se" >>> ----------------------------- >>> Scale Factor 1.0000 Shift 0.0000 S. D. >>> 0.0000 >>> Overall B 0.0000 Shift 0.0000 S. D. >>> 0.000 >>> ------------------------------**----------------- >>> Refinement Parameter = 0.000000 >>> Anomalous Refinement Parameter = 0.000000 >>> ------------------------------**----------------- >>> >>> ====== CYCLE 4 ==============================** >>> ============================= >>> >>> One more thing Mlphare did not giving me anamolous shift for individual >>> Se site. Please guide me and suggest me your valuble ideas to overcome this >>> problem. >>> >>> Thank you >>> Appu >>> >>> >> >
