Hi Thomas, With regard to selections, sometimes a residue has missing atoms or is non-standard amino acid. In the first case it is matched with another residue in a second structure during the alignment and then when I try to fit the two selections of atoms from the two structures I get the following error:
Calculating RMSD between pocket of model 2hduA and 2r9wA. > ExecutiveRMS-Error: Atom counts between selections don't match (799 vs 797) > Executive: Error -- no atoms left after refinement! > RMSD = -1.000000 Can you think of a clever way to exclude amino acids with missing atoms or non-standard ones from pair_fit() or rms_cur()? Best, Thomas On Fri, 22 Feb 2019 at 12:32, Thomas Holder <thomas.hol...@schrodinger.com> wrote: > Hi Thomas, > > In general, the PyMOL API should raise pymol.CmdException if things go > wrong. But in case of cmd.pair_fit() this wasn't happening (see my fix that > I pushed few minutes ago: > https://github.com/schrodinger/pymol-open-source/commit/b26d91c40d20344fef511ea9d6bb664a93f1bb4a > ) > > cmd.select() correctly raises an exception, so if you want to make a > script more robust against selection failures, you could always create a > named selection first to check if it's valid. > > tmpsele1 = cmd.get_unused_name('_sele1') > try: > cmd.select(tmpsele1, someexpression, 0) > except pymol.CmdException: > print('invalid selection') > finally: > cmd.delete(tmpsele1) > > > Cheers, > Thomas > > > On Feb 22, 2019, at 12:11 PM, Thomas Evangelidis <teva...@gmail.com> > wrote: > > > > Hi Thomas, > > > > This is great! I can even include more atom types in the selection. > > Just for the record, is it possible to catch PyMOL exceptions like > "Selector-Error" from within a Python script? Is there any general strategy > to select which exception type to look for? In the past, I was catching > exceptions from 'tmalign' with "except AssertionError:" which doesn't work > for "Selector-Error". > > > > Best, > > Thomas > > > > > > -- > > ====================================================================== > > Dr Thomas Evangelidis > > Research Scientist > > IOCB - Institute of Organic Chemistry and Biochemistry of the Czech > Academy of Sciences > > Prague, Czech Republic > > & > > CEITEC - Central European Institute of Technology > > Brno, Czech Republic > > > > email: teva...@gmail.com > > website: https://sites.google.com/site/thomasevangelidishomepage/ > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. > > -- ====================================================================== Dr Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en> Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/> Brno, Czech Republic email: teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/
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