Hi, Am I missing a trick to get my Arginines planar?
I took a reasonably refined PDB (no non-planar arg) (coming out of PHENIX) and noticed a series of close contacts so did some limited “sphere refine” against my 2.9A EM map and now I have fewer close contacts but gained 5 non-planar Arginines (sidechain) according to the PDB deposit review. I’ve seen this before. There is some problem in coot with the Arg refinement restraints. Original is green and sphere refined is yellow – looking down the guanidinium group and the NE hydrogen is wonky. [A close up of a network Description automatically generated] If I “send in the bond angles” then the NE hydrogen straightens out but the NH1/2 hydrogens go off axis. Heidi ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/