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November 2021

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Re: [cctbxbb] [git/cctbx_project] master: Reduce2: place NH3 only at residue with resseq 1. (765881e87b)
by Pavel Afonine 11 Nov '21

11 Nov '21

What if chain starts with a number different than 1 (people tend to number chain residues in many different ways, even using negative numbers, and they claim they have valid reasons to do so)? iotbx.pdb.hierarchy has a clear definition of the chain. So I'd suggest adding NH3 to the fist residue of the chain, no matter what that residue number is. Pavel On 11/10/21 14:03, CCTBX commit wrote: > Repository : https://github.com/cctbx/cctbx_project/ > On branch : master > Link : > https://github.com/cctbx/cctbx_project/commit/765881e87b5982c3b68e8dcd8c0e0… > > ------------------------------------------------------------------------ > > > commit 765881e87b5982c3b68e8dcd8c0e00c61c5b5600 > Author: dcliebschner <dcliebschner(a)lbl.gov> > Date: Wed Nov 10 14:03:06 2021 -0800 > > Reduce2: place NH3 only at residue with resseq 1. > > > ------------------------------------------------------------------------ > > > 765881e87b5982c3b68e8dcd8c0e00c61c5b5600 > mmtbx/hydrogens/reduce_hydrogen.py | 19 +- > mmtbx/hydrogens/tst_add_hydrogen.py | 196 ++++++++--------- > mmtbx/hydrogens/tst_add_hydrogen_2.py | 383 > ++++++++++++++++------------------ > 3 files changed, 282 insertions(+), 316 deletions(-) > > Diff suppressed because of size. To see it, use: > > git diff-tree --root --patch-with-stat --no-color > --ignore-space-at-eol --textconv --ext-diff --cc > 765881e87b5982c3b68e8dcd8c0e00c61c5b5600 > ------------------------------------------------------------------------ > > To unsubscribe from the CCTBX-COMMIT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCTBX-COMMIT&A=1 > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCTBX-COMMIT&A=1> >

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