Hi Fei: I once had the same error message when using an EM map as an MR model. To make this work, you need to change your map's axis order from XYZ to whatever is appropriate (in my case it was ZXY) and also change the spacegroup to P1 using the CCP4 program "maputils".
In the CCP4i GUI, you do as follows: 1) Go to maputils: "Map and Mask Utilities" -> "Edit/Rotate Maps & Masks". 2) Choose "Edit a map/mask file" for a "map" file. 3) Choose your map as input and choose an appropriate output file name. 4) Under the "Edit file" section, enter "Space group" as 1 and "Change axis order to" ZXY. You can get this from mapman's header when you load the map or CCP4 log file header from the failed SFall run. Alternatively, you could try all possibilities in the drop-down list. SFall should run fine using the output map from maputils. Best, Vish -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Fei Li Sent: Sunday, November 10, 2013 4:33 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] help on preparing EM map for mask generation and molecular replacement Dear experts, I'm planning to use a EM map to generate a mask for density modification and also potentially use it in molecular replacement. But I'm stuck on how to make this EM map to behave now. The original EM map was a reconstruction from 2D helical tube. The file was huge (containing several layer of the protein) and ended with .map. Our computation collaborator had already cut out a dimer, which is what I'm interested in, and put it into a small unit cell just slightly bigger than the dimer density. this file is ended with .mrc. I can open both file with coot and chimera fine. I tried to convert the dimer map into a .mtz file but when I try to use any of the ccp4 program (sfall, mapman etc), I always get error message on something like "map and mask grid samplings do not match", "Fatal disagreement between input info and map header" or "Incorrect sampling grid factors 40 29 45". I'm thinking it may be the unit cell that it is already in. But as I'm not familiar with Chimera, I couldn't figure out how to remove it. Also, how to choose and/or specify a proper grid? Any suggestion on how to make this EM map to work is high appreciated. Thank you very much! Best regards, Fei Fei LI Graduate Assistant 310 Biochemistry Building Department of Biochemistry and Molecular Biology Michigan State University East Lansing, MI 48824
