Hello,
When I run coot in order to read the experimental MTZ corresponding
to the PDB I am viewing, I got the following messages (attached is long
lines original log):
---
command: (refmac-for-phases-and-make-map
"/home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz"
"/DERIV_AU/DERIV_AU/FP" "/DERIV_AU/DERIV_AU/SIGFP")
(refmac-for-phases-and-make-map
"/home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz"
"/DERIV_AU/DERIV_AU/FP" "/DERIV_AU/DERIV_AU/SIGFP")
(molecule-name 0)
(calc-phases-generic
/home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz)
INFO:: Creating directory coot-refmac
(write-pdb-file 0 "coot-refmac/refmac-for-phases.pdb")
got args: pdb-in-filename: "coot-refmac/refmac-for-phases.pdb",
pdb-out-filename: "coot-refmac/refmac-for-phases-tmp.pdb",
mtz-in-filename:
"/home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz",
mtz-out-filename: "coot-refmac/refmac-for-phases.mtz",
imol-refmac-count: 0, show-diff-map-flag: 1, phase-combine-flag: 0,
phib-fom-pair: (), force-n-cycles: 0, f-col: "/DERIV_AU/DERIV_AU/FP",
sig-f-col: "/DERIV_AU/DERIV_AU/SIGFP", r-free-col: ()
Not Passing LIBIN to refmac LIBIN
DEBUG:: refmac-extra-params returns ()
INFO:: Running refmac with these command line args: ("XYZIN"
"coot-refmac/refmac-for-phases.pdb" "XYZOUT"
"coot-refmac/refmac-for-phases-tmp.pdb" "HKLIN"
"/home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz" "HKLOUT"
"coot-refmac/refmac-for-phases.mtz")
INFO:: Running refmac with these data lines: ("MAKE HYDROGENS NO" ""
"NCYCLES 0" "" "" "" "WEIGHT AUTO" "LABIN FP=FP SIGFP=SIGFP")
environment variable: SYMOP: #f
environment variable: ATOMSF: #f
environment variable: CLIBD: #f
environment variable: CLIB: #f
---
I am afraid coot is refining my molecule instead of just displaying the
map. Am I right?
Thanks a lot,
Francois.
command: (refmac-for-phases-and-make-map
"/home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz"
"/DERIV_AU/DERIV_AU/FP" "/DERIV_AU/DERIV_AU/SIGFP")
(refmac-for-phases-and-make-map
"/home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz"
"/DERIV_AU/DERIV_AU/FP" "/DERIV_AU/DERIV_AU/SIGFP")
(molecule-name 0)
(calc-phases-generic /home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz)
INFO:: Creating directory coot-refmac
(write-pdb-file 0 "coot-refmac/refmac-for-phases.pdb")
got args: pdb-in-filename: "coot-refmac/refmac-for-phases.pdb",
pdb-out-filename: "coot-refmac/refmac-for-phases-tmp.pdb", mtz-in-filename:
"/home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz", mtz-out-filename:
"coot-refmac/refmac-for-phases.mtz", imol-refmac-count: 0, show-diff-map-flag:
1, phase-combine-flag: 0, phib-fom-pair: (), force-n-cycles: 0, f-col:
"/DERIV_AU/DERIV_AU/FP", sig-f-col: "/DERIV_AU/DERIV_AU/SIGFP", r-free-col: ()
Not Passing LIBIN to refmac LIBIN
DEBUG:: refmac-extra-params returns ()
INFO:: Running refmac with these command line args: ("XYZIN"
"coot-refmac/refmac-for-phases.pdb" "XYZOUT"
"coot-refmac/refmac-for-phases-tmp.pdb" "HKLIN"
"/home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz" "HKLOUT"
"coot-refmac/refmac-for-phases.mtz")
INFO:: Running refmac with these data lines: ("MAKE HYDROGENS NO" "" "NCYCLES
0" "" "" "" "WEIGHT AUTO" "LABIN FP=FP SIGFP=SIGFP")
environment variable: SYMOP: #f
environment variable: ATOMSF: #f
environment variable: CLIBD: #f
environment variable: CLIB: #f
