For anyone who has found this thread, I've taken some time and put together an alignment + RMSD script for Pymol (using BioPython). You can find it on GitHub, here <https://github.com/nclement/cvc-scripts/tree/master/alignment> . It's a bit overkill, and only handles single chain proteins, but it's quite robust if it fits your needs.
On Wed, Jul 4, 2018 at 3:05 PM Thomas Holder <thomas.hol...@schrodinger.com> wrote: > Hi Nathan, > > I have some insights for this issue. Basically the long gaps between the > selected parts become too expensive in the alignment scoring. Changing e.g. > the gap extension penalty leads to the expected result: > > # default is extend=-0.7, lowering to -0.6 > super gold & contact_all, test, cycles=0, object=super, extend=-0.6 > > I think PyMOL's handling of selection gaps during the alignment could be > improved, they should be handled different from regular alignment gaps. > > Cheers, > Thomas > > > On Jun 28, 2018, at 2:14 PM, Thomas Holder < > thomas.hol...@schrodinger.com> wrote: > > > > Hi Nathan, > > > > Thank you very much for the files and instructions. I can reproduce the > problem. I haven't seen this before and don't know yet what's going wrong, > we will investigate. > > > > Cheers, > > Thomas > > > >> On Jun 28, 2018, at 10:50 AM, nclem...@cs.utexas.edu wrote: > >> > >> The alignment in this example is nearly perfect. Even the residues left > >> out of the fitting have perfect matches at the sequence level (as can be > >> seen by saving the super object and turning on the sequence alignment > and > >> contact_all). > >> > >> PyMOL>load 1AY7_u.pdb, test > >> CmdLoad: "1AY7_u.pdb" loaded as "test". > >> PyMOL>load 1AY7_b.pdb, gold > >> CmdLoad: "1AY7_b.pdb" loaded as "gold". > >> PyMOL>select contact_rec, gold & chain R & (all within 10 of gold & > chain > >> L) & n. ca > >> Selector: selection "contact_rec" defined with 33 atoms. > >> PyMOL>select contact_lig, gold & chain L & (all within 10 of gold & > chain > >> R) & n. ca > >> Selector: selection "contact_lig" defined with 33 atoms. > >> PyMOL>select contact_all, contact_rec + contact_lig > >> Selector: selection "contact_all" defined with 66 atoms. > >> PyMOL>super gold & contact_all, test, cycles=0 > >> MatchAlign: aligning residues (66 vs 185)... > >> MatchAlign: score 143.882 > >> ExecutiveAlign: 58 atoms aligned. > >> Executive: RMS = 0.524 (58 to 58 atoms) > >> > >> <1AY7_u.pdb><1AY7_b.pdb> > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. > >
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