Hi Kamil, The "Selection" field uses "polymer & ..." by default, which excludes ions. You can use a selection which includes ions instead, for example "all", "not solvent", or something like "(polymer | name CAL) & ...".
Here an example that works for me: fetch 1rx1 alter elem Ca, resn="CAL" alter elem Ca, name="CAL" In the APBS Electrostatics panel, use "(polymer | name CAL) & 1rx1" as the selection and "--ff=CHARMM" as pdb2pqr command line option. Hope that helps. Cheers, Thomas On Mon, Nov 1, 2021 at 9:21 PM Kamil Steczkiewicz <[email protected]> wrote: > > Hi, > How to include Ca/Zn ions when using APBS built into Pymol? I'm switching to > CHARMM in command line options; CHARMM has CAL and ZN2 atoms already defined > in the DAT file. But there's still no difference in electrostatics maps with > and without ions in the structure. Also, the default 'prepared01' object > lacks the ions. > Thanks for any clues, > Kamil > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/[email protected] > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/[email protected] Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
