Thanks, Eleanor! what i really want to do with this script is to compare ligand binding sites from many structures in several space groups. So, I want to move coordinates and density onto one reference molecule. Since we ran into issues, I used this dimer structure as a simple test case.
The script you outlined, only recreates the same density w/o any rotation. mapmask \ mapin AB_full-cell.ccp4 \ xyzin B.pdb \ mskout B.msk \ << eof border 5 eof maprot \ mapin AB_full-cell.ccp4 \ mskin B.msk \ mapout B_rot.map \ << eof MODE to AVER rota euler 152.440 110.243 28.112 TRANS -42.212 5.510 -57.243 end eof Btw, I had to remove the rota euler 0 0 0 / trans 0 0 0 lines. Maprot complained about too many operators. The odd thing -to me- is that when I shift a map around molecule B or the dimer (mapmask with border 5) with a small amount ( euler 1 0 0 or trans 0.5 0.5 0.5) the map does not look jagged at the edges of the molecule, while it does when I rotate the full amount to match B on A: maprot \ wrkin AB-5.map \ mapout AB_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 1 0 0 TRANS 0 0 0 end eof Cheers, Jan On Mon, Mar 25, 2019 at 3:49 AM Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: > 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 >> > -- 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
