Hi all, thanks for the feedback. Suggestions like coot or pymol won't work for us well, since we will have to do this with dozens of structures/maps.So, I'd rather have this scripted.
Still running into some issues that I think relate to maprot. My understanding is that I first have to create a map covering molecule B that I want to map on A. Checking the extend of the map in chimera confirms that this worked: mapmask \ mapin 2mol_2mFo-DFc.map \ xyzin 2mol_B.pdb \ mapout 2mol_2mFo-DFc_B.map \ << eof border 5 eof Next, I need to rotate/translate the map in maprot. Since in maprot, mapin requires a map that covers the unit cell, I use wrkin and 'mode to' as below. In this script, the cell and grid values are the same mapdump provides me for the map. The rotation and translation are from superpose, RMSD of that superposition is 0.5Å. maprot \ wrkin 2mol_2mFo-DFc_B.map \ mapout 2mol_2FoFc_rot.map \ << eof CELL xtal 61.0100 142.3600 68.2800 90.0000 97.1980 90.0000 GRID xtal 100 228 112 MODE to AVER rota euler 152.440 110.243 28.112 TRANS -42.212 5.510 -57.243 eof The issue now is that the superposed map for the center of molecule A looks great. Towards the edges of the molecule it gets weaker, does not match up with the molecule or stops entirely. Again, molecule and maps between A and B, as visualized in Coot by NCS hopping, are very similar. I am still quite puzzled by what is happening. I guess I am missing something in maprot. Any input would be appreciated. This is public data, so I would be happy to share the data. Cheers, Jan On Wed, Mar 20, 2019 at 9:26 PM Jan Abendroth <[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 > > -- Jan Abendroth Emerald Biostructures Seattle / Bainbridge Island, WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
