Hi Jan,
Sorry I didn't read your script earlier. If you change your mapmask command to output a map instead of a mask it may work for you: mapmask \ mapin 2mol_2mFo-DFc.map \ xyzin 2mol_B.pdb \ MAPOUT B.map \ << eof border 2 eof then you should get a map that covers the whole molecule B, and whatever happens to share the parallelepiped volume with it. This is essentially what the FFT method I mentioned in previous email does: modify the origin and the extent of the output map to cover the PDB, not really masking the map based on the atoms. If you want to further mask the map to cover atoms of B only, then you can use UCSF chimera -- volume viewer -- zone to selected atoms --save as mrc density map (same as ccp4 map, just different extension and no crystallographic SG). Some shifting may be needed, but it should be trivial. I also did a little test with the mskout option of mapmask. The generated mask file does look strange, or, not what a naive user would expect maybe? Zhijie ________________________________ From: CCP4 bulletin board <[email protected]> on behalf of Jan Abendroth <[email protected]> Sent: Thursday, March 21, 2019 12:26 AM To: [email protected] Subject: [ccp4bb] map rotation Hi all, this should be easy, scripting the rotation of a map. Purpose for this is: Superimpose several structures of the same protein that crystallized in different space groups, and then drag the maps along. As a simple test, I took a dimeric protein and try to superimpose molecule B along with the map on molecule A. The execution should be straightforward: a) take a map that covers the unit cell (fft), b) generate a mask around molecule B (mapmask), c) apply rotation/translation that I obtain from superimposing molecule B on molecule A. The issue is that the obtained map covers both molecule A and B (not a big deal), more importantly, it cuts of certain areas on both molecules. Molecule A and B have low RMSDs (0.5Å). I must be missing something fairly obvious, have not been able to see what. Feedback would be much appreciated. Scripts are below. Thanks! Jan mapmask \ mapin 2mol_2mFo-DFc.map \ xyzin 2mol_B.pdb \ mskout 2mol_2mFo-DFc_2mol_B.msk \ << eof border 2 eof maprot \ mapin 2mol_2mFo-DFc.map \ mskin 2mol_2mFo-DFc_2mol_B.msk \ wrkout 2mol_2mFo-DFc_rot.map \ << eof MODE from AVER ROTA euler 152.440 110.243 28.112 TRANS -42.212 5.510 -57.243 eof -- Jan Abendroth Seattle / Bainbridge Island, WA, USA home: Jan.Abendroth_at_gmail.com<http://Jan.Abendroth_at_gmail.com> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
