Yes, it's "mode sfcalc" in refmac:
echo mode sfcalc |\
refmac5 mapin density.map hklout density.mtz
As for automating sfall, I've found that using SFSG 1 makes it so all
you need to do is make sure the map has the axis order for P1. I have a
script that checks for this error and re-runs sfall with the right axis
order in the event it comes up:
http://bl831.als.lbl.gov/~jamesh/pickup/ano_sfall.com
-James Holton
MAD Scientist
On 5/14/2020 3:28 PM, Bernhard Rupp wrote:
Thanks to all. Mapmask works. Yes the order to change to is ZXY. Map
from coefficients indeed looks like the directly loaded map, jus the
scale is different (I supplied no reference PDB)
The remaining issue is - a pain to automate.
I tried Refmac- there is a mention of an sfall mode and I tried to
input the map and a reference HKL .. In that case, refmac simply stops
after reading the map.
If I add a XYZIN to scale the map, I get a mtz but not from the map,
which is never read.
I am not even sure – this is from the EM part in the instructions – if
this is intended to work in this fashion.
Has somebody tried that successfully with an Xray map?
Many thanks again, BR
*From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> *On Behalf Of
*Alejandro Buschiazzo
*Sent:* Thursday, May 14, 2020 15:10
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Using SFall for map conversion
Oh…maybe I suggested the wrong order then (Y X Z - for SG 20) ?
…I do realize YXZ is not an XYZ cyclic permutation (whereas ZXY is)…I
dug it from an old script of mine, so now rechecked the FFT doc …but
yes, FFT says that Y X Z is the std axis ordering for SGs higher-than
18…I’m probably missing something silly here (any clue James?)
Best, ale
On May 14, 2020, at 6:45 PM, James Holton <jmhol...@lbl.gov
<mailto:jmhol...@lbl.gov>> wrote:
Use mapmask first:
echo axis Z X Y |\
mapmask mapin1 old.map mapout new.map
For reasons I'm sure made sense at one time, sfall does not seem
to know how to automatically re-order the map axes.
Also, it is generally a good idea to expand to P1 first, and use
"SFSG 1" in sfall. There are still some "gotcha" space groups in
the SFALL code for density near cell edges. I can't remember
which ones now because years ago I started using SFSG 1 and the
problem went away.
-James Holton
MAD Scientist
On 5/14/2020 1:44 PM, Bernhard Rupp wrote:
Hi Fellows,
I am failing on conversion of a ccp4 map to mtz using Sfall
I provide as a scale reference a mtz with FP SIGFP and R free
All cell constants and SG 20 and map headers seem to agree.
But I receive following warning:
*** WARNING - your map spacegroup is different to the program
default one ***
and later
>>>>>> CCP4 library signal library_file:Cannot <file:///Cannot>open
file (Warning)
raised in tmpfile() failed, opening normal file instead. <<<<<<
INPUT X USED AS X
INPUT Y USED AS Z
INPUT Z USED AS Y
Which then leads to the imho - given above- justified complaint:
Check map header agrees with fixed requirements for SFcalc for
this spacegroup.
Check Nxyz 180 200 120 180 200 120
Check map header agrees with fixed requirements for SFcalc for
this spacegroup.
Check Iuvw 3 2 1 3 1 2
<B><FONT COLOR="#FF0000">
SFALL: **** Fatal disagreement between input info and map header
How do I fix this ?
In principle all the information is there to do the job…
Many thx, BR
------------------------------------------------------
Bernhard Rupp
Crystallographiae Vindicis Militum Ordo
http://www.hofkristallamt.org/
b...@hofkristallamt.org <mailto:b...@hofkristallamt.org>
+1 925 209 7429
+43 676 571 0536
------------------------------------------------------
Many plausible ideas vanish
at the presence of thought
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