Hi Jan, I guess you might be seeing a flat cut surface on the maps? It might be that the map’s extent is not covering the protein molecule, which is usually the case. When you rotate crystallographic maps it is usually no longer possible to take adjacent unit cells to continue the density on the boundaries as the crystallographic periodicity is lost.
You may try computing maps that cover “all atoms in PDB “ using the map tool (FFT) from the ccp4 interface. Maps generated this way cover your protein portion supplied in the PDB file. Alternatively you can measure the extremes of your A and B monomers and change the extents of the maps by hand. BTW, UCSF chimera does not automatically extend maps as COOT does. So you can easily see what is the extent of your current map using chimera. Zhijie On Mar 21, 2019, at 12:27 AM, Jan Abendroth <[email protected]<mailto:[email protected]>> wrote: 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
