Creating a mtz file with Fobs for structure in pdb

Download the Structure factor file as a mmciF formatted file using: Download files -Structure-factor(text) option
 

In ccp4i go to the : reflection data utilities - Convert to/modify/extend MTZ option

This is the front-end for the cif2mtz program.

In the menu pick Import relection file in mmCIF format

Give it the cif file you downloaded . The downloaded file may have the *.cif.txt extension. Change the filter appropriately and read in the file. The cif file is a txt file which should contain a  lot of information about the cell , symmetry , spacegroup and other crystallographic information.

For now we will need the cell and symmetry. Look at the cif file in a text editor or alternatively get the cell and symmetry from the page corresponding to the structure on the pdb

In my case I dont have the cell dimensions etc in the cif file so I get it from the pdb summary page where the download link was.

feed that to the appropriate columns in the ccp4i GUI conversion window and it should spit out an mtz file.

Common problems:

The cif file does not have an rfree flag .

Symptom: In the loop for the reflections you should see an "o" and an "f" indicating if the observation was used for the refinement or used as part of the rfree for eg

1 1 1    0    0   72      79.57     2.25    6331.50   353.70 o

                                                                                 |-----> This o indicates this reflection was used in refinement

1 1 1    0    0   78     124.84     4.08   15586.20  1001.00 f

                                                                                   |----> This was part of the rfree

Solution :generate an rfree flag from scratch AND write to the auhtor of the pdb file asking him to provide you the exact mtz file hes used for the refinement.

The cif file is a swapped file :

Solution write a script to convert this around or use this script useage 

rectify_cif.py -ciffile [input.cif]