On 27/03/16 17:23, Yaowang Li wrote:

Dear all,

I want to convert a density map (mrc) to structure factor (mtz) using the script in the EM_fitting_tools, while I faced a problem, I have no idea about it.

the script mrc2mtz mainly calls the two programs: mapmask and sfall. the mapmask succeeded to convert the map to a intermediate map "tmp.map", but sfall failed to convert it to structure factor. Here is the output of the program sfall.

###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 7.0: SFALL                    version 7.0 :   ##
 ###############################################################
 User: unknown  Run date: 27/ 3/2016 Run time: 18:08:29


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.

<!--SUMMARY_END--></FONT></B>

 Memory allocation (logical name, type, elements):
   MEMSIZE R      5000000
   MEMSIZE I      5000000
 **CCPOPN ERROR**  FORMATTED      OLD     file open failure on unit  45
 Logical name: ATOMSF, File name: ATOMSF
 No such file or directory

It looks like you didn't properly initialize your CCP4 environment.

But this is the old way of doing it - here's how we do it now:


# this makes shifted.pdb and shifts.txt and masked_fs.mtz
#
refmac5 XYZIN my.pdb MAPIN input.map XYZOUT shifted.pdb << eof
MODE SFCALC
SFCALC SHIFT
END
eof