Hi, this can be a start: http://cci.lbl.gov/docs/cctbx/doc_maps_boxing/ There are a lot of boxing options: with and without masking (with many masking options: smooth masks, etc), around atom selection, per NCS etc.. Pavel
On Fri, Aug 5, 2022 at 2:30 AM Evgenii Osipov <[email protected]> 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 > ######################################################################## 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/
