Hmm - I find maprot extremely confusing, but remember a wrkmap does not use any symmetry so maybe that is why some is lost.
I would have done this, but I havent tested it. And the documentation is SERIOUSLY confusing!! Do I understand you want to ADD the density for mol B to that of Mol A mapmask mapin whole-cell.map xyzin A.pdb mskout A-mol.msk Then maprot mapin whole-cell.map mskin A-mol.msk ! only density withing this mask is interesting mapout A-mol.map MODE to AVER rota euler 0 0 0 ! to pick up mol A density trans 0 0 0 rota euler 152.440 110.243 28.112 ! to rotate map by B to A rotation TRANS -42.212 5.510 -57.243 end On Mon, 25 Mar 2019 at 04:58, Jan Abendroth <jan.abendr...@gmail.com> wrote: > 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 <jan.abendr...@gmail.com> > 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 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
