Jan, you my wish to try MAIN as an alternative "http://www-bmb.ijs.si/";. The superimposition parameters obtained from either FatCat or MAIN directly are directly saved into the form that is used in map rotation and translation. Maps do not have to be in a unit cell (it may be simpler though).
The scripts are generated during setup of an interactive session when generating NCS operators (in the case the molecules do not contain highly identical sequences FatCat/CE interface has to be used). The scripts can be called during non-interactive use too. If you have any questions or you need additional information to the manual please ask. best, dusan Dr. Dusan Turk, Prof. Head of Structural Biology Group http://stef.ijs.si/ Head of Centre for Protein and Structure Production Centre of excellence for Integrated Approaches in Chemistry and Biology of Proteins, Scientific Director http://www.cipkebip.org/ e-mail: dusan.t...@ijs.si phone: +386 1 477 3857 Dept. of Biochem.& Mol.& Struct. Biology fax: +386 1 477 3984 Jozef Stefan Institute Jamova 39, 1 000 Ljubljana,Slovenia Skype: dusan.turk (voice over internet: www.skype.com > On 26 Mar 2019, at 01:00, CCP4BB automatic digest system > <lists...@jiscmail.ac.uk> wrote: > > Date: Sun, 24 Mar 2019 21:57:45 -0700 > From: Jan Abendroth <jan.abendr...@gmail.com> > Subject: Re: map rotation > > 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 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
