This can do done, but I suspect it is much easier using COOT tools - then you can output a map from COOT. Will check later .. Eleanor
On Thu, 21 Mar 2019 at 07:28, Zhijie Li <zhijie...@utoronto.ca> wrote: > Hi Jan, > > > Sorry I didn't read your script earlier. If you change your mapmask > command to output a map instead of a mask it may work for you: > > > mapmask \ > > mapin 2mol_2mFo-DFc.map \ > > xyzin 2mol_B.pdb \ > > MAPOUT B.map \ > > << eof > > border 2 > > eof > > then you should get a map that covers the whole molecule B, and whatever > happens to share the parallelepiped volume with it. This is essentially > what the FFT method I mentioned in previous email does: modify the origin > and the extent of the output map to cover the PDB, not really masking the > map based on the atoms. > > > If you want to further mask the map to cover atoms of B only, then you can > use UCSF chimera -- volume viewer -- zone to selected atoms --save as mrc > density map (same as ccp4 map, just different extension and no > crystallographic SG). Some shifting may be needed, but it should be trivial. > > > I also did a little test with the mskout option of mapmask. The > generated mask file does look strange, or, not what a naive user would > expect maybe? > > > Zhijie > > > ------------------------------ > *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Jan > Abendroth <jan.abendr...@gmail.com> > *Sent:* Thursday, March 21, 2019 12:26 AM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] map rotation > > 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 > > > ------------------------------ > > 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 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
