Hi Joe, There can be atoms without coordinates. In particular, when loading mmCIF files, PyMOL fills in dummy-CA atoms for missing residues, to provide a complete sequence display in the sequence viewer.
"alter" iterates over all atoms, including those without coordinates. "iterate_state" only includes those *with* coordinates. Your issue can be handled in several ways: 1) Make a selection on the atoms with coordinates in state 1: select mysele, state 1, enable=0 alter mysele, b = next(di) spectrum b, selection=mysele 2) Or just remove atoms which don't have coordinates in state 1: remove not state 1 alter all, b = next(di) spectrum b See "Coordinates" section here: https://pymolwiki.org/index.php/Selection_Algebra Cheers, Thomas > On Sep 12, 2019, at 6:09 PM, Heffron, Joseph <joseph.heff...@marquette.edu> > wrote: > > Hello all, > > I am trying to color several proteins by different factors, e.g., distance > from a given point (here the origin). To do this, I replace the q-factor (or > b-factor) with my variable of choice. However, most of my files have one or a > few residues that are for some reason not affected by the alter_state (e.g., > pdb = 1ihm). I can't see any distinction in these residues compared to the > others. > > example code: > > fetch 1ihm > alldist = [] > iterate_state 1, all, alldist.append((x**2+y**2+z**2)**0.5) > di = iter(alldist) > alter all, b = next(di) > spectrum b > > Thank you, > Joe > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
