Dear CCP4, Thanks for the answers — now I could to do map masking using Gemmi. It is worth to post the Python script in case someone else would need it too:
import gemmi mtz = gemmi.read_mtz_file(‘map.mtz’) m = gemmi.Ccp4Map() m.grid = mtz.transform_f_phi_to_map(‘2FOFCWT’,’PH2FOFCWT’,sample_rate=3) m.update_ccp4_header() ligand = gemmi.read_structure(‘ligand.pdb’) m.set_extent(ligand.calculate_fractional_box(margin=3)) m.write_ccp4_map(‘masked.ccp4’) -- Evgenii Osipov Laboratory for Biocrystallography, Department of Pharmaceutical Sciences, KU Leuven O&N2 mobile: +32 484 38 26 01 > On 5 Aug 2022, at 11:30, Evgenii Osipov <e.m.osi...@gmail.com> wrote: > > Dear CCP4 community, > > I am looking for a way to cut a fragment of electron density around specified > set of atoms using Python script. In CCP4 I found MAPMASK, which could cut > fragment of electron density within specified region around input PDB: > #!/bin/bash -f > > $CCP4/bin/mapmask \ > MAPIN tmp.map \ > MAPOUT masked.map \ > XYZIN ligand.pdb \ > << > eor > BORDER 3 > eor > > Of course I could call this shell script from Python script using > subprocess, but it looks like unnecessary overcomplication. > > I wonder if the same task could be completed by Python script using either > CCTBX or Gemmi. May be someone had this problem in the past and could share > their example? > > > > Kind regards, > > -- > > Evgenii Osipov > > Laboratory for Biocrystallography, > Department of Pharmaceutical Sciences, > KU Leuven O&N2 > > mobile: +32 484 38 26 01 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
