Hi Francois,
your mtz file doesnt appear to have any phases, so Coot (or whoever)
cannot make a map. What Coot cleverly tries to do in such a case is to
use calculated phases from the given pdb (and mtz) file. So it runs
refmac with the pdb and mtz to retrieve this phase information. There is
no refinement within refmac going on as such (see below: NCYCLES 0).
B
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.
